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 Yuting Fang (ANU, Australia), Nan Yang (ANU, Australia), Andrew W. Eckford (York, Canada), and Rodney A. Kennedy (ANU, Australia).
Posted to arXiv - Modeling Interference-Free Neuron Spikes with Optogenetic Stimulation
Our paper "Modeling Interference-Free Neuron Spikes with Optogenetic Stimulation" was posted to arXiv. This paper considers how to predict the charging and recovery times when neurons following the Izhikevich model 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 last year under the title "Timing Control of Single Neuron Spikes with Optogenetic Stimulation".
Submissions are now open for the 2019 IEEE Global Communications Conference (IEEE GLOBECOM). I am chairing the track on Molecular, Biological and Multi-Scale Communications. Submissions are due 15 April 2019 via https://edas.info/N25091. You can find a text version of the call in the detail of this news item, or get the PDF from here.
Posted to arXiv - On the Analysis of Bacterial Cooperation with a Characterization of 2D Signal Propagation
Our paper "On the Analysis of Bacterial Cooperation with a Characterization of 2D Signal Propagation" was posted to arXiv. This paper derives new results on diffusion with degradation over a 2D environment and applies them to a model for bacteria quorum sensing. We then use approximations to estimate the expected density of cooperating bacteria. The paper was co-authored with Yuting Fang, Nan Yang, and Andrew W. Eckford, and submitted to IEEE ICC 2019.
Tutorial on Molecular Communication at IEEE GLOBECOM
I will be helping to deliver a tutorial on molecular communication at this year's IEEE GLOBECOM in Abu Dhabi, UAE. The full title is "Molecular Communication: Methods, Simulations, and Experiments" It will be presented with Andrew Eckford (York), Yansha Deng (KCL), and Nariman Farsad (Stanford). The tutorial will be held on Sunday, 9 December from 2pm-5:30pm.
Abstract: This tutorial introduces the emerging field of molecular communication wherein chemical signals are used to connect "tiny" machines such as living cells, synthetic biological devices and swarms of micro-scale robots. The tutorial begins with an overview of molecular communication systems and how they are modeled; each has a Transmitter, the Propagation Channel, and the Receiver, just as in a conventional communication system. Specific channel and noise models are presented and the derivation of channel impulse responses is discussed. Signal processing via chemical and genetic circuits is described. An overview and demonstration of specialized simulation tools is provided. The tutorial concludes with a discussion of the recent experimental implementations of molecular communication, and some of the most important open problems in this exciting new area.
My section of the tutorial will be on simulation methods, and will include a demonstration of the AcCoRD simulator.
To see about about the tutorial, including registration, please see here: http://globecom2018.ieee-globecom.org/program/tutorials#tut10
Paper Accepted - Algorithm for Mesoscopic Advection-Diffusion
The paper "Algorithm for Mesoscopic Advection-Diffusion" (link to arXiv version) was accepted for publication in IEEE Transactions on NanoBioscience. This paper was co-authored with Dimitrios Makrakis. The full implementation of the proposed algorithm is included in the AcCoRD simulator (Actor-based Communication via Reaction-Diffusion).
Posted to arXiv - A Novel A Priori Simulation Algorithm for Absorbing Receivers in Diffusion-Based Molecular Communication Systems
Our paper "A Novel A Priori Simulation Algorithm for Absorbing Receivers in Diffusion-Based Molecular Communication Systems" was posted to arXiv. This paper shows how a Monte Carlo type approach can be used to efficiently simulate surface absorption in microscopic particle-based simulations. Compared with the usual method for simulating microscopic surface absorption, the proposed scheme can speed up simulations by many orders of magnitude with a very small loss in accuracy. The paper was co-authored with Yiran Wang and Nan Yang and submitted for journal publication. An implementation of this algorithm is included in the AcCoRD simulator (Actor-based Communication via Reaction-Diffusion).
Papers Accepted for IEEE GLOBECOM 2018
The following papers papers were accepted for presentation at the 2018 Global Communications Conference (IEEE GLOBECOM):
- "Modeling Duct Flow for Molecular Communication" (link to arXiv version). This paper was co-authored with Wayan Wicke, Tobias Schwering, Arman Ahamdzadeh, Vahid Jamali, and Robert Schober.
"Transceiver Observations in Asymmetric and Symmetric Diffusive Molecular Communication Systems". This paper was co-authored with Lanting Zha, Yansha Deng, Maged Elkashlan, and Arumugam Nallanathan.
GLOBECOM will be in Abu Dhabi from 9-13 December, 2018.
Posted to arXiv - Algorithm for Mesoscopic Advection-Diffusion
Our paper "Algorithm for Mesoscopic Advection-Diffusion" was posted to arXiv. The title is pretty straightforward; we present and implement an algorithm to simulate both diffusion and flow within the spatial SSA (also know as the spatial Gillespie or mesoscopic simulation algorithm). These kinds of simulations divide an environment into virtual subvolumes and track the numbers and types of molecules present in each subvolume. They have long been used to simulate reaction-diffusion systems, and our contribution adds bulk fluid flow. The paper was co-authored with Dimitrios Makrakis and submitted for journal publication. The full implementation of the algorithm is included in the AcCoRD simulator (Actor-based Communication via Reaction-Diffusion).
Special Issue on Mathematical Modeling, Implementations, Applications and Simulators for Molecular Communications
I helped to guest edit a Special Issue for Nano Communication Networks on "Mathematical Modeling, Implementations, Applications and Simulators for Molecular Communications". Five articles were accepted and they have been published in the June 2018 issue. A free link (will work until 5 July) to the editorial is here: https://authors.elsevier.com/a/1X3D-6hBrE2MlB