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Research - Biophysical Communication Engineering (BioPhysComm) Lab

TLDR: We work on biophysical signal propagation, cellular signal processing, and molecular communication engineering.

Overview

SIMBA Project

Simulation Tools for Molecular Communication

Presentation Links

Overview

We're interested in the signalling cues that drive the behaviour of living cells and other microscale processes. Our long-term objective is to use communications and signal processing tools to improve the understanding of biophysical processes and how to interact with them at a microscopic level.

As examples, we're interested in answers to the following questions:

  • Could we disrupt signalling between cells? This could be used to prevent a biofilm from forming or a cancerous tumour from developing.
  • Could we support a diseased system to maintain signal integrity and prevent degeneration?
  • Could we safely add a network of nanorobots to a body without disrupting natural signalling processes?

Ultimately, we hope that this research can be coupled with advancements in nanotechnology to aid in the advancement of medical treatments and other applications that rely on the release and detection of molecules.

Our underlying research lens is communications engineering. We look at molecular communication as an inter-disciplinary domain at the intersection of communications theory, physical chemistry, and biology. Progress in this field can improve our understanding of biological processes while also enabling the design and deployment of novel communication networks in biological and fluid environments. Novel systems based on molecular communication could advance applications such as targeted drug delivery, distributed environmental monitoring, and lab-on-a-chip systems.

Below are summaries of on-going projects. You can also refer to our contributions on the Publications page.


SIMBA: Signal Propagation and Information in Microscale Biological Applications

The SIMBA project (Signal Propagation and Information in Microscale Biological Applications) seeks to address the gap between the contributions of molecular communications research and applications in relevant disciplines. It is establishing a communications engineering hierarchy for the characterisation and control of cellular behaviour and decision-making.

This project is funded by the UK's EPSRC.


Hierarchy for Mapping Communication to Microscale Behaviour

The proposed hierarchy is comprised of 5 levels (as introduced in A Survey of Molecular Communication in Cell Biology: Establishing a New Hierarchy for Interdisciplinary Applications, 2021). The levels are:

  1. Physical Signal Propagation - models how molecules physically propagate, whether they are transmitted by some “device” or come from the ambient environment.
  2. Physical/Chemical Signal Interaction - the interface between molecules and the “devices” that send or receive them, including how those molecules are involved in local signalling pathways, e.g., chemical binding kinetics.
  3. Signal-Data Interface - the interface between the physical signal at “devices” and its representation as quantified data.
  4. Local Data Abstraction - the quantification of information and what it means at a local “device”, e.g., what activity or state has been observed or what action is to be taken.
  5. Application - the aggregate behaviour of communicating devices, e.g., quorum sensing by bacteria and other cells.

Hierarchy Example

The proposed communication level hierarchy applied to an example cellular signaling environment.

The proposed communication level hierarchy is applied above to an example cellular signalling environment (Image from A Survey of Molecular Communication in Cell Biology: Establishing a New Hierarchy for Interdisciplinary Applications, 2021). The communicating devices are two cells separated by extracellular space. In this scenario, Level 1 describes the signal propagation across the extracellular space. Levels 2-4 describe the biochemical pathways, signal-data interface, and data abstraction within the individual cells, respectively. Level 5 describes the overall behaviour requiring communication between the two cells.


SIMBA Project Case Studies

The SIMBA project is applying the proposed hierarchy to two case studies:

  1. Bacterial Behaviour. We will apply the proposed hierarchy to a heterogeneous population of S. coelicolor bacteria mutants produced in the lab of Dr Christophe Corre in the School of Life Sciences.
  2. Organ-on-a-Chip Systems. We will demonstrate the proposed hierarchy’s potential for pharmaceutical systems by investigating the impact of noisy signal propagation on metabolic regulation in an organ-on-a-chip system developed by AstraZeneca Sweden.

Simulation Tools for Molecular Communication

Simulation tools play an important role in verifying analysis and understanding system models. To this end, we are developing AcCoRD (Actor-based Communication via Reaction-Diffusion) as an open source project for simulating molecular communication systems.


Presentation Links

Here are some presentation slides describing the area and some of our contributions:

  • 2021-02 MBCom - "Molecular Communication Essentials: Building Blocks for Analysis and Simulation of Diffusion-Based Systems" - slides from a 2-hour tutorial that I presented at the 1st International Symposium on Molecular and Biological Communications, which was hosted virtually by VNIT Nagpur in February 2021. I go into the basics of diffusion-based channel modelling, a statistical description of reaction-diffusion, and algorithms to implement a molecular communication simulation.
  • 2020 (Newer) Introduction to Molecular Communication - the latest version of my introductory slides on nanonetworking and molecular communication. This set comes from a presentation that I gave as a seminar for the ES96T Wireless Communications module at Warwick. My 2013 slide set appears to be getting a rather high number of downloads; this one has similar ideas but includes summaries of some of my work up to about 2017 (PhD+PostDoc).
  • 2019-04 EU Mol Comm Workshop Tutorial – "Simulation Methods for Molecular Communication" – a tutorial delivered to the 4th Workshop on Molecular Communication in Linz, Austra, in April 2019.
  • 2017-01 Memorial University Presentation – “Using Molecular Communication to Understand and Improve Chemical Signaling” – a presentation to Memorial University (St. John’s, Newfoundland and Labrador, Canada) in January 2017.
  • 2016-07 University of Toronto Presentation – “Finding Common Ground: Channel Analysis and Receiver Models for Diffusive Molecular Communication” – a presentation to the University of Toronto (Toronto, Ontario, Canada) in July 2016.
  • 2013 Introduction to Molecular Communication – an introduction to nanonetworking and diffusive molecular communication. This was presented twice in 2013 as a guest lecture to the MIMO course at the Institute for Digital Communications (IDC) at FAU Erlangen-Nuremberg (Erlangen, Germany).