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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

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

Mon 19 Nov 2018, 14:33 | Tags: molecular communication, conference, simulation, tutorial

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).

Tue 23 Oct 2018, 17:06 | Tags: molecular communication, simulation, journal

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).

Wed 05 Sep 2018, 08:59 | Tags: molecular communication, arxiv, simulation

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).

Fri 01 Jun 2018, 08:35 | Tags: molecular communication, arxiv, simulation

Paper Accepted for IWMBMC workshop at IEEE SECON 2018

The paper "A New Simulation Algorithm for Absorbing Receiver in Molecular Communications" (link to arXiv version) was accepted for presentation at the 2018 International Workshop on Molecular, Biological and Multiscale Communications, which is being held in conjunction with the IEEE International Conference on Sensing, Communication and Networking (IEEE SECON). This paper was co-authored with Yiran Wang and Nan (Jonas) Yang. The workshop will be in Hong Kong from 11-13 June, 2018.

Wed 04 Apr 2018, 09:18 | Tags: molecular communication, conference, simulation