2nd Workshop on Molecular Communications

Dublin, Ireland – 9th – 11th May of 2017

Organizing Committee:

General Co-Chairs:

Alan Davy

Mauro Femminella

TPC Co-Chairs:

Pietro Lio

Gianluca Reali

Eduard Alarcon

Josep Sole Pareta

Raul Cid-Fuentes

Wouter Tavernier

Paolo Gresele

Murat Kuscu

Michael Taynnan Barros

Steering Committee:

Sasi Balasubramaniam

Ozgur Akan

The 2nd Workshop on Molecular Communications is being held in Dublin City, Ireland on the 9th to 11th of May 2017. Following on from the great success of the first workshop, this workshop will provide strategic development of Molecular Communications research in Europe with a focus on broadening the reach of the community into border disciplines. Disciplines we wish to attract speakers from include (but are not limited to)

Microfluidics, Synthetic Biology, Pharmacology, Inter/Intra Cellular Communication, Chemical Networks, Bio Medicine, etc.

The Workshop will also run three expert lead technical sessions focusing on hot topics in the area of Molecular Communications. This will provide the research community an opportunity to meet and share their research, vision and experience in the area of Molecular Communications. The workshop will host three strategic sessions promoting panel lead discussion and debate in areas related to young researchers in Molecular Communications, stimulating industry engagement in Molecular Communications and a research roadmap for molecular communications.

The workshop will also incorporate a Molecular Communications school encompassing three focused tutorials aimed at young researchers wishing to engage in the molecular communications discipline. This workshop also aims to attract other complementary disciplines to this emerging research domain, such as synthetic biology and microfluidics.

Registration is now open via [Eventbrite]

Student Travel Grants

We will be offering a small number of student travel grants to assist young researchers attending the School. Please complete the form provided and return to circle@fet-circle.eu (At the latest by the 30th March 2017) to be considered. We will inform students of a decision within 2 weeks of receiving the application.


May 9th, 2017
09:30-10:30 Opening and Keynote

Prof. Tom Lenaerts,  Université Libre de Bruxelles

Information theory and the regulation of protein activity

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10:30 – 11:00 Break and Posters
11:00 -13:00 Tutorial 1 (Dr. Gianluca Reali CIRCLE – MolComML Toolkit)

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13:00 – 14:00 LUNCH
14:00 – 15:30 Technical 1

“On molecular communications for Microfluidic Networks”

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From Microfluidic Communications to Microfluidic Networking:

but I still haven’t found what I’m looking for 

(Giacomo Morabito, University of Catania, Italy)

A Microfluidic Communication Link: Definition, Analysis and Experimentation(Andrea Zanella, University of Padova, Italy)

Towards Push-Button Solutions: Design Automation for Microfluidic Chips (Werner Haselmayr, Johannes Kepler University Linz, Austria)

MakerFluidics: Microfluidics for the Masses (Ryan Silva, Boston University, US)

Potentials in Combining Microfluidics and Metabolic Studies (Pietro Lio, University of Cambridge, UK)

15:30 – 16:00 BREAK
16:00 – 17:00 Panel 1

Young Researchers in Molecular Communications

[chair] Dr. Sasitharan Balasubramaniam (TSSG), Prof. Ozgur Akan (University of Cambridge), Prof. Ilanko Balasingham (Norwegian University of Science and Technology), Dr. Goksel Misirli (Keele University)

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17:00 – 19:00 Social Reception @ the Science Gallery
May 10th, 2017
09:30 – 10:30 Keynote

(Prof. Boris Kholodenko,  University College Dublin)

Molecular communications in four dimensions

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youtube Go to the video (part 2)

10:30 – 11:00 Break and Posters
11:00 – 13:00 Tutorial 2 (Dr. Mirela Alistar – Microfluidics)

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13:00 – 14:00 LUNCH
14:00 – 15:30 Technical 2

“MolCom for therapeutic local drug delivery: the oncology case”

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Mobile Molecular Communication Networks for Targeted Drug Delivery (Tadashi Nakano, Osaka University, Japan)

Optical and multimodal interfaces for molecular communication systems

(Costas Pitris, University of Cyprus, KIOS CoE)

Molecular detection using electrochemical nanosensors: considerations for optimised device performance

(Alan O’Riordan, Tyndall National Institute, Ireland)

Communication theoretical approaches to model neuronal networks and predict functions (Ilangko Balasingham, Oslo University Hospital, Norway)

Enabling Models for Experimental Validation and Therapeutic Translation of Molecular Communication Systems

(Andreani Odysseos, EPOS-Iasis and University of Cyprus, Cyprus)

15:30 – 16:00 BREAK
16:00 – 17:00 Panel 2

Stimulating Industry Engagement in Molecular Communications

[chair] Dr. Pietro Liò (Cambridge University), Dr. Mirela Alistar (Hasso Plattner Institute), Sheryas Shah (Nokia Bell Labs, US); Prof. Filippo Castiglione (National Research Council of Italy); Emre Ozer (ARM, UK)

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17:00 – 20:00 City Tour Event
20:30 – 24:00 Banquet Meal @ Fade Street Social
May 11th, 2017
09:30 – 10:30 Keynote (Dr. Richard Morris, John Innes Centre)

Molecular Communication by Calcium

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10:30 – 11:00  BREAK
11:00 – 13:00 Tutorial 3 (Dr. Filippo Castiglione, Simulating Biological Networks)

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13:00 – 14:00 LUNCH
14:00 – 15:30 Technical 3

“Molecular communications: modelling languages and simulators”

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Simulation of Nanoscale communications on Cyber Physical Systems, Luca Felicetti (CIRCLE, University of Perugia)

Challenges in the Design on Microscale (Electronic) Systems,

Elena Blokhina (EU, UCD Dublin)

GPU-based Parallel Simulation for Molecular Communications,

Tuna Tugcu (Turkey, Bogazici University)

Upconversion phenomenon as a viable tool for nanoscale communication channel modelling,

Valeria Loscri (Inria Lille-Nord Europe)

Reproducibility of Biological System Designs,

Goksel Misirli (Keele University)

15:30 – 16:00  BREAK
16:00 – 17:00 Panel 3

Roadmap for Molecular Communications Research

[chair] Eduard Alarcon (Universitat Politècnica de Catalunya, Spain); Prof. Tom Lenaerts (Université Libre de Bruxelles, Belgium), Dr. Alan Davy (TSSG, Ireland), Dr. Andreani Odysseos (University of Cyprus), Prof. Richard Morris (John Innes Centre, UK)

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17:00 – 17:30 Closing Session


Dublin City was founded as a Viking settlement in 988 AD, the Kingdom of Dublin became Ireland’s principal city following the Norman invasion. Now Dublin is a vibrant city, home to the Silicone Docks located at the Grand Canal, which has the highest concentration of high-tech companies outside the US.


This event is co-funded by the Science Foundation Ireland under grant no. 16/CW/4535 and H2020 FETOpen CIRCLE project with EU funding from the European Union’s Horizon 2020 research and innovation programme under the grant agreement No. 665564.


Prof. Tom Lenarts
Tom Lenaerts 2015Next to Prof. Lenarts position as an Associate Professor at the Université Libre de Bruxelles, he is also a Research Professor at the VUB.   His research projects are principally concerned with Computational Biology problems and this at different biological scales.


Title: Information theory and the regulation of protein activity

Language-based communication transpires at diverse scales of life.  Whereas human words are formed by sounds, cells employ a language of molecules to communicate.  Parallels are often drawn between this molecular language and the information processing performed by simple gates in integrated circuits. This parallel is by no means just a metaphor: Shannon’s information theory can be used to measure the fidelity of the information exchange between and within proteins, which act in unison as relays and switches in signal transduction pathways.  The difficulty nonetheless is to identify which residues and dynamics processes are involved in the information exchange through their structures.

In the last decade, we have developed a predictive approach that allows us to identify from structural data the set of residues implicated in transducing a signal throughout the structures of simple protein domains (e.g. PDZ, SH2 and SH3 domains), an approach we also have expanded to understand information flows between proteins. While explaining the approach I will show that our predictions are confirmed by data describing the effect of peptide binding on the dynamic properties of these domains and that these communication patterns are conserved within those domain families.  This approach allowed us to show how sidechain dynamics of particular residues in the SH2 domain of the Src-like protein Fyn are crucial for the regulation of this protein’s activity, a feature that was never identified before with potential medical applications.

This computational biology research generates novel insights into how protein activity is regulated, providing an important next step to understanding the molecular language.  At the same time, it underlines the importance of information theory and the computational modelling of molecular communication to shed light on a range of interesting biological questions.

Prof. Boris Kholodenko

Boris Kholodenko is an SFI Stokes Professor of Systems Biology at University College Dublin. He moved to Dublin in 2009 to organize the Institute of Systems Biology Ireland, with Prof. Walter Kolch. He was previously a Professor at the Thomas Jefferson University in Philadelphia and the Free University in Amsterdam. Boris graduated summa cum lau de from the Moscow Institute of Physics and Technology. He received his PhD in Mathematical Biophysics from that Institute and a D.Sc. from the Moscow State University. He developed the first systems biology model of the Epidermal Growth Factor Receptor signalling pathway, predicted the existence of intracellular gradients of signalling activities (which were later discovered experimentally) and developed a novel method (termed Modular Response Analysis) to unravel molecular connections in signalling and gene networks from perturbation responses. His current studies focus on using personalised dynamic models, which are based on patient genetic profiles, to uncover fundamental hidden mechanisms of varying treatment responses.

Title: Molecular communications in four dimensions

The advancements in “omics” technologies have yielded large inventories of genes, transcripts, proteins, and metabolites. The challenge is to find out how these molecular entities communicate to regulate cellular responses to external and internal cues. Physics-based models provide insight into the intricate relationships between stimuli and responses, revealing mechanisms that enable networks to amplify signals, reduce noise and generate bistable dynamics and oscillations. In this talk, I review how cellular functions are encoded by the spatiotemporal dynamics of signalling and gene networks that specify biological decisions. I illustrate an integrative, modular approach termed Modular response Analysis to infer the circuitry of cellular signaling and gene networks from experimentally measured network responses to perturbations. Further I show how bistability at the biochemical level of small GTPases results in the bistable behaviour of cell migration.  Finally, I show that fundamental thermodynamics principles can explain why dimerization of RAF kinases confers resistance to clinically used RAF inhibitors in melanoma.  Physics-based models suggest and experiments demonstrate how two inhibitors ineffective on their own when combined can abolish this drug resistance.

Prof. Richard Morris

Richard_Morris7.pngRichard completed a degree in Mechanical Engineering before obtaining his BSc and MSc in Physics, specialising in theoretical physics and molecular quantum mechanics. He carried out his PhD research at the European Molecular Biology Laboratory (EMBL) in Hamburg in computational protein crystallography. He went on to post-doc positions at the MRC-LMB working on Bayesian software development and the European Bioinformatics Institute (EMBL-EBI) working on protein shape descriptors . In 2005, Richard joined the John Innes Centre (JIC) as a group leader in computational biology. Richard played a key role in building up the Department of Computational and Systems Biology, which he headed until 2013. He is now associate research director at JIC and programme leader for Plant Health. Richard’s research focusses on computational approaches for studying intra and intercellular communication in plants. He has published over 60 research papers in peer-reviewed journals such as Plant Cell, PNAS, Nature and Science.

Title: Molecular Communication by Calcium

Developmental changes are induced in plants by their interaction with microbes. A striking example of this is nodule organogenesis. Nodules are plant-derived structures formed by legumes under nitrogen-limiting conditions that allow them to form a symbiotic relationship with host-specific strains of nitrogen-fixing bacteria, called rhizobia. The interaction with the rhizobia is governed by fine-tuned chemical communication process. Within the plant, developmental changes are initiated by changes in calcium concentration in the peri-nuclear region. These symbiotic calcium signals are thought to activate downstream processes that lead to cell wall remodelling, infection thread formation and nodule organogenesis.

In this talk I will focus on the integrated use of mathematical modelling as part of a larger, interdisciplinary programme to unravel the mechanisms underlying the generation, transmission and decoding of symbiotic calcium oscillations that lead to induced developmental changes. I will demonstrate how simply ‘toy models’ can lead to functional insights that would not be easy to obtain otherwise. I will highlight predictions made by the models, their strengths and their limitations, as well as the challenges ahead.