The Biophysical Communication Engineering Lab has moved from Warwick to Memorial University (St. John's, Newfoundland and Labrador, Canada), where Adam Noel has been appointed as an Associate Professor in the Department of Electrical and Computer Engineering. The new website is https://www.engr.mun.ca/~adamnoel.

Links to the new page (and to its webpages) have been add throughout this site, which will no longer be regularly updated.

Our paper "Spheroidal Molecular Communication via Diffusion: Signaling Between Homogeneous Cell Aggregates" (arXiv link) has been accepted to appear in IEEE Transactions on Molecular, Biological, and Multi-Scale Communications. We model two spheroids as transmitter and receiver in a diffusion-based molecular communication system. Both spheroids are modeled as spheres whose porous features are approximated with a lower diffusion coefficient than that of the surrounding fluid medium. We derive the end-to-end channel impulse response and characterize the corresponding communications performance.

This paper is an output of the SIMBA project and is the first journal paper of Mitra Rezaei's PhD. It was also co-authored with Hamidreza Arjmandi from our group, in addition to Mohamad Zoofaghari (Yazd University, Iran) and our SIMBA project collaborators at AstraZeneca Sweden (Kajsa Kanebratt, Liisa Vilen, David Janzen, and Peter Gennemark).

We're very pleased to share that Dr Hamidreza Arjmandi, who was a member of our group from November 2021 to November 2023, has started a new faculty position as an Assistant Professor in Bioinformatics at the Institute of Cancer and Genomic Sciences in the College of Medical and Dental Sciences, University of Birmingham. Hamidreza made many contributions to the SIMBA Project and we wish him great success in his new role.

Our paper "Spheroidal Molecular Communication via Diffusion: Signaling Between Homogeneous Cell Aggregates" has been posted to arXiv. We model two spheroids as transmitter and receiver in a diffusion-based molecular communication system. Both spheroids are modeled as spheres whose porous features are approximated with a lower diffusion coefficient than that of the surrounding fluid medium. We derive the end-to-end channel impulse response and characterize the corresponding communications performance.

This paper is an output of the SIMBA project. It was co-authored with Mitra Rezaei and Hamidreza Arjmandi from our group, in addition to Mohamad Zoofaghari (Yazd University, Iran) and our SIMBA project collaborators at AstraZeneca Sweden (Kajsa Kanebratt, Liisa Vilen, David Janzen, and Peter Gennemark).

We contributed to the online educational resource Best Readings in Molecular Communication, which has been issued by the IEEE Communications Society. It is a reading list of notable textbooks, special issues, and a selection of the most significant research papers in the field of molecular communication. Most of the listed resources are from within the last 10 years. The list was compiled to help newcomers to the field - both from within and outside the communications engineering community - become quickly familiar with the fundamentals and major advancements of molecular communication.

This resource was co-authored with Dadi Bi and Yansha Deng (King's College London) and Nan Yang (Australian National University).

Our paper "DeepGEEP: Data-Driven Prediction of Bacterial Biofilm Gene Expression Profiles" has been posted to bioRxiv. This paper considers petri dish experiments where a signaling molecule that can stimulate fluorescence is added to a freshly-plated bacteria sample. The fluorescence is triggered by gene expression and requires that the local signaling molecule concentration is within a suitable range. We try to predict where fluorescence will occur based on the location where the signaling molecules are dropped onto the dish. A convolutional neural network is applied to simulated data to make the predictions.

This paper is an output of the SIMBA project. It is first-authored by our group member Hamidreza Arjmandi and co-authored with Christophe Corre (University of Warwick School of Life Sciences and Department of Chemistry) and Hamidreza Jahangir.

Many thanks and best wishes to Nadezhda Briantceva who just completed her 3-month visit to our research group. It was great to have Nadya here to start a new collaboration on the fluid dynamics of lab-on-chip systems. The stay was too short but at least we still managed to have some fun (lab group trip to play footgolf in the second photo).

Four contributions from our research group were presented at ACM NanoCom 2023 which we also had the great pleasure of hosting here at Warwick! Thanks to an agreement between ACM and the University of Warwick, all four are freely available with Open Access from the ACM Digital Library.

The regular paper Biophysical Model for Signal-Embedded Droplet Soaking into 2D Cell Culture presents our group's first experimental work with bacteria where we develop a model for liquid droplets soaking into an agar plate. We derive a channel response to describe the molecule dynamics within the agar and the molecules that get absorbed by bacteria growing on top of the agar. We use a basic experiment to estimate the droplet soaking parameters and use particle simulations for the diffusion and absorption processes. The paper was co-authored with Christophe Corre (University of Warwick School of Life Sciences and Department of Chemistry).

Furthermore, we presented 3 poster papers:

1. Role of Channel Capacity in Biofilm introduces the usefulness of the notion of communication channel capacity in biofilms. Yanahan Paramalingam was the first author.
2. Generalized Model of Neurite Trafficking presents a Markov chain model for molecules being transported inside vesicles along the axon of a neuron. This paper was co-authored with Anne Straube (Warwick Medical School). Mahir Taher was the first author.
3. On the Order Statistics of Chemical Kinetics and Their Role in Molecular Communication presents our first work to model the timing of chemical reaction events.

We've made our group's first pre-print submission to bioRxiv. We posted our paper 3D Cell Cultures Amplify Diffusion Signals. This paper models the amplification of diffusion signals that occurs across the boundary of an organoid immersed in liquid. With a combination of theory and experiments, we verify the amplification factor as a function of diffusion coefficients inside and outside the organoid. The main result is that, on a very short timescale, organoids act like sponges and can make measurable changes to nutrient concentrations in the surrounding environment. This provides useful insight for lab-on-chip systems and other applications that have dense collections of cells.

This paper is an output of the SIMBA project. It is first-authored by our group member Hamidreza Arjmandi and co-authored with our SIMBA project collaborators at AstraZeneca Sweden (Kajsa Kanebratt, Liisa Vilen, and Peter Gennemark).

Our paper "Biophysical Model for Signal-Embedded Droplet Soaking into 2D Cell Culture" has been posted to arXiv. This paper presents our group's first experimental work with bacteria where we develop a model for liquid droplets soaking into an agar plate. We derive a channel response to describe the molecule dynamics within the agar and the molecules that get absorbed by bacteria growing on top of the agar. We use a basic experiment to estimate the droplet soaking parameters and use particle simulations for the diffusion and absorption processes. This work will be the foundation for us understanding how signals can propagate within and between surface bacterial communities. The paper was co-authored with Christophe Corre (University of Warwick School of Life Sciences and Department of Chemistry).