4th Workshop on Molecular Communications

Keynote 1: Information processing and distributed computation in plant organs » (PDF)

Prof. Georg Bassel Chair in Plant Computational Biology, University of Birmingham UK

George Bassel is a Chair in Plant Computational Biology at The University of Birmingham, UK. His lab seeks to understand how information from the environment is processed within complex plant tissues. The research integrates both experimental and theoretical approaches, and lies at the interface between biological and computational sciences.

Abstract
Plant growth and development is tightly coupled to the environment. These external inputs are processed within organs in order to optimize the timing of key decisions, such as the termination of dormancy or commencement of flowering. In order to better understand how collections of cells in plants process information, parallels and differences between these naturally evolved organisms and engineered computational systems are being examined. Specifically, whether the control principles of distributed computation also apply to information processing in plants. By viewing plant organs as integrated systems of interacting cells, we are mapping intercellular connectivity into networks to reveal the multicellular “circuitry” plants use to compute. Integrating these topological templates with mathematical models capturing the genetic programs that operate within individual cells enables the impact of each cell organization and communication rate on the timing of emergent decision-making to be examined. The development of further theory to identify the bounds of information processing in plants will enable their transformation into rational distributed computing devices.

Keynote 2: Mesoporous silica nanoparticles for drug delivery: towards nanoscale communication

Dr. Yolanda Salinas Assistant Professor at the Institute of Polymer Chemistry (ICP), Johannes Kepler University Linz

Dr. Yolanda Salinas was graduated as Chemical Engineer from University of Valencia in 2008 and under-took her PhD in 2009 at Polytechnic University of Valencia, Spain, in the research group of Prof. Ramón Martínez-Máñez. In 2013 she moved to London as Marie Curie Experienced Researcher inside an international network, NANODRUG, coordinated by Professor M. Resmini, in the School of Biological and Chemical Sciences, Queen Mary University of London, to work in the synthesis and characterisation of novel organic-inorganic polymeric nanogels for transdermal drug delivery applications in skin cancer diseases. Since September 2015 she holds a position for 6 years as university assistant at the Institute of Polymer Chemistry (ICP) coordinated by Professor O. Brüggemann, at the Johannes Kepler University of Linz, Austria. As a young researcher with a broad range of knowledge and experience in the development and characterization of different kind of nanomaterials, that include different types of nanoparticles, from sensor to stimuli responsive organic nanogels and molecularly imprinted polymers for biomedical applications, she has published in the last years 15 papers (two of them highly cited reviews). In 2017, she was awarded by the Linz Institute of Technology (JKU, Austria) with her first Young Career Project, ”Degradable hybrid organosilica phosphazene mesoporous nanoparticles for nanomedicine” where she is Principal Investigator.

Abstract
Multifunctional hybrid materials based on mesoporous silica nanoparticles (MSNs) have been selected for many years as appealing nanoplatforms for drug delivery applications. Their thermal stability, a rigid framework which prevents premature degradation of the drug, and easy chemical attachment of responsive units that exhibit a control over undesirable premature drug release, then reducing the side effects of conventional systems, are features that makes them stand out candidates. The design of different pH, temperature, or even light-sensitive organic functionalities or polymers to control the release of chemotherapeutics through a selective ”close-opening gate-like mechanism” under pathological conditions typical of cancer cells, has been attracting great interest in field of nanomedicine. In this context and inspired by the scientists aims of mimicking the communication in nature, a remarkable growth has appeared for a deep understanding of the mechanisms at molecular level of the chemical messengers or the communication between cells. At the nanoscale, this idea is recently being investigated and the control over the transmission and receiving of information between nanoparticles is a challenging area that could endow a path towards personalized therapeutics and medical therapy by an interdisciplinary collaboration between telecommunication and computer engineers and chemists.

Keynote 3: Molecular communications and interplay of neuron-astrocyte networks » (PDF)

Prof. Jari Hyttinen Professor at the Faculty of Medicine and Health Technology Tampere University

Professor Jari Hyttinen is full professor and head of BioMediTech unit at the Faculty of Medicine and Health Technology, Tampere University. His research group Computational Biophysics and Imaging Group develops novel computer simulations (in-silico) on cellular biophysics and in-vitro based electrophysiology and 3D imaging methods for future personalized medicine. Previous he has been a visiting researcher at University of Pennsylvania, University of Tasmania, Duke University and as visiting professor at University of Wollongong 2017 and ETH Zurich 2018. He has been active on scientific societies including Chair (2001-2004) of the Finnish Society of Medical Physics and Biomedical Engineering and president (2015-2017) of the European Alliance on Medical and Biological Engineering Sciences EAMBES. EU. He has been also active on organization of conferences, latest as chair of the joint European Conference on Medical and Biological Engineering and Nordic-Baltic Meeting on BME. He is also EAMBES Fellow. He has graduated over 110 MSc and 18 PhDs, co-author of more than 390 scientific papers including over 150 referee journal papers and some patents that has also been transferred to companies including http://www.injeq.com that he was also a co-founder.

Abstract
Recent evidence in neuroscience research has strengthened the concept of molecular communication and interplay between neurons and astrocytes. The tripartite synapses and astrocyte gliotransmission in neuronal communication has evoked increasing interest. Though the astrocyte and neuronal network functions are interrelated, they are fundamentally different in their signaling patterns and time scales at which they operate. We have composed biologically plausible computational models of singe astrocyte, astrocyte network and astrocyte-neuron network level interactions. On single astrocyte level we have developed a finite element model of the calcium and IP3 signaling in the complex astrocyte geometry driven by the neurotransmitter input from the synapses. In network level the astrocyte and neuronal networks are interconnected by the tripartite synapses. Each astrocyte control several hundreds of synapses that trough the gliotransmission activate astrocyte calcium signaling that can evoke astrocyte network level communications. Our results on single cell level highlight the role of astrocyte morphology on the astrocyte molecular communications. Our results on network level demonstrate the role of astrocytes as regulators of network signaling. Thus highlighting the role of astrocyte interplay in neuronal molecular communications and adaptation.

Tutorial 1: Microfluidics Research at JKU » (PDF)

Werner Haselmayr, Assistant Professor<br>
Prof. Robert Wille <br>
Medina Hamidović, PhD student

Werner Haselmayr, Assistant Professor
Prof. Robert Wille
Medina Hamidović, PhD student Johannes Kepler University Linz

Werner Haselmayr received the Dipl.-Ing. (M.Sc.) degree in telematics from the Graz University of Technology, Austria, in 2007, and the Dr.techn. (Ph.D.) degree in mechatronics from Johannes Kepler University Linz, Austria, in 2013. He is currently an Assistant Professor with the Institute for Communications Engineering and RF-Systems, Johannes Kepler University Linz. His research interests include algorithm design for wireless communications, iterative pro- cessing, and molecular communications.

Robert Wille received the Diploma and Dr.-Ing. degrees in computer science from the University of Bremen in 2006 and 2009, respectively. He has been with the University of Bremen from 2006-2015 and with the German Research Center for Artificial Intelligence (DFKI) from 2013 onwards. Additionally, he worked as lecturer and guest professor at the University of Applied Science of Bremen, the University of Potsdam, and the Technical University Dresden. Since 2015, he is Full Professor at the Johannes Kepler University Linz, Austria. His research interests are in the design of circuits and systems for both conventional and emerging technologies including quantum computation, biochips, reversible circuits, and more.

Medina Hamidović has received her B.Sc. degree in electrical engineering at the University of Tuzla in 2014. Since 2017 Hamidović holds two Master’s degrees in electrical engineering from Heriot-Watt University (UK) and Budapest University of Technology and Economics (BME). At the moment, Hamidović is a Ph.D. researcher and University Assistant at the Institute for Communications Engineering and RF-Systems at the Johannes Kepler University Linz (Austria). Her research is focused on the area of molecular communications and microfluidic networks.

Abstract
Communications and networking on microfluidic chips using tiny volumes of fluids, so-called droplets, is a promising sub-field of molecular communications. In particular, microfluidic networks have been introduced as a promising concept for realizing programmable, flexible, and bio-compatible Lab-on-a-Chip devices, which can be used for example for fast and flexible drug screening. The aim of this tutorial is to bring the attention of the molecular communication community to this exciting research area and to lower its entry barrier. The tutorial will start with an accessible introduction of the fundamentals of droplet-based microfluidics. Then, we will present microfluidic switches as the key building block for microfluidic networks and discuss different network topologies. We will introduce a novel simulation tool dedicated for the fast simulation of microfluidic networks, which is based on the analogy between microfluidic networks and electrical circuits. Then, we present our in-house fast prototyping of microfluidic chips, enabling their fabrication within a couple of minutes at low-cost. The tutorial concludes with a presentation of the most important problems and we show the opportunities for researchers to contribute to this area.

Tutorial 2: Simulation Methods for Molecular Communication » (PDF)

Adam Noel Assistant Professor in the School of Engineering, University of Warwick, Coventry, UK

Adam Noel is an Assistant Professor in the School of Engineering at the University of Warwick in Coventry, UK. He received the B.Eng. degree in electrical engineering in 2009 from Memorial University in St. John’s, Canada. He received the M.A.Sc. degree in electrical engineering in 2011 and the Ph.D. degree in electrical and computer engineering in 2015, both from the University of British Columbia in Vancouver, Canada. In 2013, he was a Visiting Scientist at the Institute for Digital Communication at Friedrich-Alexander-University in Erlangen, Germany. He has also been a Postdoctoral Fellow at the University of Ottawa and the University of Montreal. His research interests are in the prediction and control of biophysical systems at a microscopic level. Dr. Noel has received several awards from the Natural Sciences and Engineering Council of Canada, including a Postdoctoral Fellowship. He also received a Best Paper Award at the 2016 IEEE International Conference on Communications.

Abstract
Molecular communication (MC) is an emerging multi-disciplinary field that applies communications engineering tools to molecular signalling. This tutorial will give a brief overview of the MC field and then consider the simulation of reaction-diffusion environments for molecular communication systems. We will describe the scales of simulation tools available, including those developed within the biophysics community. We will then present some of the specialized tools that have been developed specifically for MC. We will focus on an open source ‘sandbox’ simulation tool to make the simulation of molecular reaction-diffusion dynamics more accessible to the communications engineering research community. This tool, called AcCoRD (Actor-based Communication via Reaction-Diffusion), will be presented with live demonstrations that show how to understand and visualize common MC channels, how to test new environments, and how to assess MC system performance.

Ideation 1

Session Chair: Prof. Tuna Tugcu

The Molecular Communications community has grown over the past 10 years. The community is now aiming to form a COST Action cluster to further stimulate the community and grow its activities across Europe. During the COST Action call in 2018, a proposal to form a Molecular Communications COST Action cluster was proposed. However this proposal was not funded. This Ideation session will focus on gathering input from the community to address the concerns of the proposal and aim to develop an action plan to improve the proposal proposition and resubmit the proposal to the September 2019 call deadline. Participants of the session will be provided with the submitted proposal along with the list of reviewer comments. As all COST Actions are open to Member States to join, all participants are also encouraged to join the consortium bid for September 2019.

Ideation 2

Session Chair: Richard Morris

This session will explore recent advances in the highly interdisciplinary field of Molecular Communications with the goal of identifying commonalities and synergies between individuals and groups as well as between different areas and approaches. The session will have multiple parts consisting of open dialogue, break out groups, discussion and project development. This is the first time we are trying this type of session within the workshop and we greatly welcome your ideas and feedback.

Technical 1: Drug Delivery Models

Session Chair: Maximilian Schäfer

1. Modelling the Drug Release Kinetics of Mesoporous Silica Nanoparticles » (PDF)
Andreas Ganhör, Julian Karoliny, Dominik Lehner, Adam Noel, Yolanda Salinas, Oliver Brüggemann, Andreas Springer and Werner Haselmayr

2. Controlled Release for Diffusive Mobile Molecular Communication Systems » (PDF)
Trang Ngoc Cao, Arman Ahmadzadeh, Vahid Jamali, Wayan Wicke, Phee Lep Yeoh, Jamie Evans and Robert Schober

3. Flow-based molecular communication system for the detection of hyperviscosity syndrome » (PDF)
Luca Felicetti, Mauro Femminella and Gianluca Reali

4. Ant-behavior Inspired Intelligent NanoNet for Targeted Drug Delivery in Cancer Therapy » (PDF)
Lin, Liu, Yan and Guo

Technical 2: Applications of Molecular Communications

Session Chair: Luca Felicetti

1. Coexistence Within Communicating Biological Systems » (PDF)
Malcolm Egan, Bayram Akdeniz and Valeria Loscri

2. Agent Based Modeling of the Rhizobiome with Molecular Communication and Game Theory » (PDF)
Apostolos Almpanis, Christophe Corre and Adam Noel

3. An Iterative Approach for Estimating Information Exchange in Cell-to-cell Molecular Communication » (PDF)
Francesca Ratti, Colton Harper, Massimiliano Pierobon and Maurizio Magarini

4. A Logic Gate Model based on Neuronal Molecular Communication Engineering » (PDF)
Geoflly L. Adonias, Anastasia Yastrebova, Michael Taynnan Barros, Sasitharan Balasubramaniam and Yevgeni Koucheryav

Technical 3: Experimental Molecular Communications

Session Chair: Ethungshan Shitiri

1. Linear Duct Flow Model for Macroscale MC » (PDF)
Wayan Wicke, Vahid Jamali, Arman Ahmadzadeh, Harald Unterweger, Jens Kirchner, Georg Fischer, Christoph Alexiou and Robert Schober

2. First Practical Realization of Switching in Microfluidic Networks » (PDF)
Medina Hamidović, Uli Marta, Andreas Grimmer, Gerold Fink, Robert Wille, Helen Bridle, Andreas Springer and Werner Haselmayr

3. Modeling an Experimental Biological Modulator for Molecular Communications by Electrical Circuits » (PDF)
Maximilian Schäfer, Wayan Wicke, Laura Grebenstein, Christian Strobl, Renata Starvracakis Peixoto, Jens Kirchner, Andreas Burkovski, Georg Fischer, Robert Weigel, Rudolf Rabenstein and Robert Schober

Technical 4: Channel and Receiver Models

Session Chair: Prof. Tuna Tuğcu

1. Receiver Design using Genetic Circuits in Molecular Communication » (PDF)
R. Deniz Aksoy, H. Birkan Yilmaz, M. Sukru Kuran, Anil Wipat, A. Emre Pusane, Goksel Misirli and Tuna Tuğcu

2. Performance Enhancement of Diffusive Molecular Communications with an Apertured Plane » (PDF)
Mustafa Can Gursoy, H. Birkan Yilmaz, Ali Emre Pusane and Tuna Tuğcu

3. An Analytical Model of Diffusion in a Sphere with Semi-Permeable Boundary » (PDF)
Maximilian Schäfer and Rudolf Rabenstein

4. Analysis of Akaike’s Information Criterion for Propagation Delays in a Free-Diffusion Channel » (PDF)
Ethungshan Shitiri, H. Birkan Yilmaz and Ho-Shin Cho

5. Noise Modeling for Molecular Communication via Chemical Reactions and Diffusion » (PDF)
Bayram Cevdet Akdeniz and Malcolm Egan

4th Workshop on Molecular Communications

Linz, Austria, 16^th-18^th April 2019

Organizing Commitee

Themes

Keynotes

Tutorials

Ideation

Technicals

Linz, Austria, 16th-18th April 2019