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New Funding: Signal Propagation and Information in Microscale Biological Applications

We have successfully received funding for the project "Signal Propagation and Information in Microscale Biological Applications (SIMBA)," which has been granted by the EPSRC as a New Investigator Award at a value of £313k (£392k FEC). This will be a 30-month project starting in Spring 2021 and it will establish a communications engineering framework for describing and controlling cell signalling, behaviour, and decision-making. The framework will be applied to interdisciplinary case studies of bacteria signalling and organ-on-a-chip systems. The bacteria case study will model the emergence of antimicrobial resistance in an environment with different mutants of the S. coelicolor bacterium. The organ-on-a-chip case study will model metabolic regulation between liver and pancreatic cells, as observed in an experimental microfluidic platform. The project team includes Adam Noel as PI, Christophe Corre (Department of Chemistry and School of Life Sciences) as Co-I, and AstraZeneca as an industrial partner. We will also be hiring a postdoctoral research assistant for a 2-year term.

Tue 06 Apr 2021, 10:41 | Tags: molecular communication, funding

Paper Accepted: A Survey of Molecular Communication in Cell Biology: Establishing a New Hierarchy for Interdisciplinary Applications

Our paper "A Survey of Molecular Communication in Cell Biology: Establishing a New Hierarchy for Interdisciplinary Applications" (open access DOI) was accepted for publication in IEEE Communications Surveys & Tutorials. This paper bridges the gap between life sciences and communications engineering to promote the application of molecular communication as a methodology for applications that require communication between cells and other microscale devices. To do so, we propose a novel communication hierarchy for molecular communication signalling in cell biology. We map biological phenomena, research contributions, and open problems to the hierarchy. We also apply the hierarchy to case studies on quorum sensing, neuronal signalling, and communication via DNA. This paper was co-authored with Apostolos Almpanis from our group, in addition to Dadi Bi and Yansha Deng (King's College London), and Robert Schober (FAU, Germany).

Thu 18 Mar 2021, 10:40 | Tags: molecular communication, survey, journal

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

Our paper "Characterization of Cooperators in Quorum Sensing with 2D Molecular Signal Analysis" (link to arXiv version; here is the DOI) was accepted for publication in IEEE Transactions on Communications. This paper models quorum sensing by a community of bacteria. Each bacterium makes a single decision whether to cooperate based on the quorum sensing signal observed due to the aggregate bacterial population. We apply stochastic geometry to derive the quorum sensing channel statistics and the distribution of the number of bacteria that choose to cooperate. Derivations are verified with particle-based simulations. The paper was co-authored with Yuting Fang (Melbourne, Australia), Andrew W. Eckford (York, Canada), Nan Yang (Australian National University), and Jing Guo (Beijing Institute of Technology). An early version was presented at IEEE GLOBECOM 2019 under the title "Expected Density of Cooperative Bacteria in a 2D Quorum Sensing Based Molecular Communication System".

Sun 15 Nov 2020, 12:27 | Tags: molecular communication, journal

Posted to arXiv: A Survey of Molecular Communication in Cell Biology: Establishing a New Hierarchy for Interdisciplinary Applications

Our paper "A Survey of Molecular Communication in Cell Biology: Establishing a New Hierarchy for Interdisciplinary Applications" has been posted to arXiv. This survey provides a hierarchical framework to model communication-based behaviour in cells. We use the framework to review instances of communication in cell biological systems and identify opportunities to control behaviour and design new systems. We also apply the hierarchy to case studies of quorum sensing, neuronal signalling, and communication via DNA. In particular, the hierarchy provides a roadmap to understand how cell behaviour is informed and constrained by the propagation of molecular signals and the physical mechanisms for detecting those signals. The survey was co-authored with Dadi Bi (King's College London), Apostolos Almpanis (Warwick), Yansha Deng (King's College London), and Robert Schober (FAU Erlangen-Nuremberg, Germany).

Fri 04 Sep 2020, 09:28 | Tags: molecular communication, arxiv, survey

Paper Accepted: Modeling Interference-Free Neuron Spikes with Optogenetic Stimulation

Our paper "Modeling Interference-Free Neuron Spikes with Optogenetic Stimulation" (link to arXiv version; here is the DOI) was accepted for publication in IEEE Transactions on Molecular, Biological and Multi-Scale Communications. This paper tries to predict the charging and recovery times of neurons that follow the Izhikevich model and that are stimulated with an external current (such as by a light source in the case of optogenetics). We measure the sensitivity of the charging and recovery times as functions of the stimulation current and the Izhikevich model parameters. We also measure the distortion when we try to generate sequences of action potential spikes at frequencies that are too high for a neuron membrane to return to its resting potential before it is stimulated again. The paper was co-authored with Shayan Monabbati (Case Western, USA), Dimitrios Makrakis (uOttawa, Canada), and Andrew W. Eckford (York, Canada). An early version was presented at IEEE ICC 2018 under the title "Timing Control of Single Neuron Spikes with Optogenetic Stimulation".

Wed 22 Apr 2020, 22:09 | Tags: journal, optogenetics

Paper Accepted: Molecular Information Delivery in Porous Media

The paper "Molecular Information Delivery in Porous Media" (link to arXiv version; here is the DOI) was accepted for publication in IEEE Transactions on Molecular, Biological, and Multi-Scale Communications. We perform the first study of using a porous material as a diffusive communication channel. With the help of statistical breakthrough curves, we compare the characteristics of communication in a porous channel with that of the more familiar free space diffusion channel. One key difference is that increasing the Peclet number in a porous channel can increase the size of the tail of the channel impulse response, whereas this would decrease the size of the channel impulse response tail in the free space case. This paper was co-authored with Yuting Fang (ANU, Australia), Weisi Guo (Warwick), Matteo Icardi (Nottingham), and Nan Yang (ANU, Australia).

Wed 28 Aug 2019, 08:16 | Tags: molecular communication, journal

Paper Accepted: "Diffusive Molecular Communication in a Biological Spherical Environment with Partially Absorbing Boundary"

The paper "Diffusive Molecular Communication in a Biological Spherical Environment with Partially Absorbing Boundary" (link to arXiv version; here is the DOI) was accepted for publication in IEEE Transactions on Communications. We derive the diffusive channel response for a transmitter and receiver that are arbitrarily placed within a partially absorbing spherical shell. This paper was co-authored with Hamidreza Arjmandi and Mohammad Zoofaghari (both at Yazd University, Iran).

Wed 03 Jul 2019, 09:58 | Tags: molecular communication, journal

Paper Accepted - A Novel A Priori Simulation Algorithm for Absorbing Receivers in Diffusion-Based Molecular Communication Systems

The paper "A Novel A Priori Simulation Algorithm for Absorbing Receivers in Diffusion-Based Molecular Communication Systems" (link to arXiv version; here is the DOI) was accepted for publication in IEEE Transactions on NanoBioscience. We propose a Monte Carlo type approach to efficiently simulate surface absorption in microscopic particle-based simulations. The algorithm is shown to be very accurate when simulating with large time steps. This paper was co-authored with Yiran Wang and Nan Yang (both at ANU, Australia). An implementation of this algorithm is included in the AcCoRD simulator (Actor-based Communication via Reaction-Diffusion).

Sun 30 Jun 2019, 11:58 | Tags: molecular communication, simulation, journal

Paper Accepted - "Channel Modeling for Diffusive Molecular Communication - A Tutorial Review"

The paper "Channel Modeling for Diffusive Molecular Communication - A Tutorial Review" (link to arXiv version; here is the DOI) was accepted for publication in Proceedings of the IEEE. We do an extensive review of the end-to-end communication channel models that are available for diffusive molecular communication systems, as well discuss simulation methods and experimental testbeds. It should be a helpful resource for anyone interested in working in this area, whether you are new to the field or an experienced member. This paper was co-authored with colleagues at FAU (Germany): Vahid Jamali, Arman Ahmadzadeh, Wayan Wicke, and Robert Schober.

Fri 21 Jun 2019, 09:39 | Tags: molecular communication, journal, tutorial

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

The paper "Symbol-by-Symbol Maximum Likelihood Detection for Cooperative Molecular Communication" (link to arXiv version; here is the DOI) was accepted for publication in IEEE Transactions on Communications. We propose different methods of maximum-likelihood-based detection when a fusion centre combines observations of diffusing molecules by a collection of receivers. This paper was co-authored with Yuting Fang (ANU, Australia), Nan Yang (ANU, Australia), Andrew W. Eckford (York, Canada), and Rodney A. Kennedy (ANU, Australia).

Mon 20 May 2019, 15:47 | Tags: molecular communication, journal

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