Elsevier

Nano Communication Networks

Volume 4, Issue 4, December 2013, Pages 181-188
Nano Communication Networks

DIRECT: A model for molecular communication nanonetworks based on discrete entities

https://doi.org/10.1016/j.nancom.2013.08.004Get rights and content

Abstract

A number of techniques have been recently proposed to implement molecular communication, a novel method which aims to implement communication networks at the nanoscale, known as nanonetworks. A common characteristic of these techniques is that their main resource consists of molecules, which are inherently discrete. This paper presents DIRECT, a novel networking model which differs from conventional models by the way of treating resources as discrete entities; therefore, it is particularly aimed to the analysis of molecular communication techniques. Resources can be involved in different tasks in a network, such as message encoding, they do not attenuate in physical terms and they are considered 100% reusable. The essential properties of DIRECT are explored and the key parameters are investigated throughout this paper.

Introduction

With the introduction of nanoscale communication networks, or nanonetworks  [1], molecular communication has become an alternative approach to electromagnetic communication at the nanoscale. Although different communication protocols have been proposed to implement molecular communication  [2], [24], [23], [15], they all rely on the use of small molecules, including ions and hormones, which are physically transported from the transmitters to the receivers. For instance, in diffusion-based molecular communication, the transmitted particles propagate by means of diffusion in a fluid medium  [20]. Diffusion-based molecular communication encompasses several techniques, such as calcium ion (Ca2+) signaling  [25], one of the most important communication mechanisms among living cells, and pheromonal communication  [26].

This paper introduces DIRECT, a general model which allows the analysis of molecular communication techniques by modeling the molecules used to encode messages as resources. Formally, DIRECT can be defined as a set of techniques, models and protocols developed to efficiently operate a network which utilizes and relies on discrete entities, i.e., resources. These resources are used to encode messages and they act as information carriers over a medium in a confined environment.

Most of the previous work on molecular communication treats molecules as entities which disperse in an unconfined environment. As opposed to this, DIRECT considers a closed environment where a group of transmitter and receiver nanomachines communicate by exchanging a finite set of molecules, which are interpreted as resources. Since the amount of resources is fixed and remains constant throughout the network lifespan, nanomachines need to harvest resources in order to transmit new messages. This harvesting need of nanomachines represents the main idea behind DIRECT and, as it is later shown, it represents one of the main constraints of the performance of the nanonetwork.

If properly harvested, any resource in a molecular communication nanonetwork located in a confined space can be reused. This allows the infinite recirculation of resources, i.e., the continuous use and harvest cycle, and naturally introduces the concept of resource conservation in a nanonetwork based on molecular communication. In an ideal case, the harvesting of resources by nanomachines would allow the perpetual operation of the network without the need of creating new resources. Our intention with DIRECT is to model the recirculation of resources in a molecular communication nanonetwork, to investigate its properties and to define its limits and capacity.

The issue of resource harvesting has been widely studied in the electromagnetic communication domain  [36], [37]. However, the concept of electromagnetic energy does not completely overlap with the concept of resources in DIRECT, since electromagnetic waves attenuate as they propagate throughout space (for instance, because of absorption by obstacles in the wave path). Therefore, we think that DIRECT is the first model that will allow modeling the recirculation of resources in molecular communication nanonetworks. Please note that this document provides an introduction to DIRECT, explaining general concept and main properties as well as constitutional elements of the model. Some preliminary results from experiments and related observations are given in order to constitute the first steps of a future analytical model.

The rest of this document is organized as follows. In Section  2, we provide the information about the usage of Ca2+ ions in molecular communication and how ER and Mitochondria harvests Ca2+ for future use. In Section  3 the state of the art and related works are briefly explained by stressing the differences with respect to DIRECT. In Section  4, different operating environments are introduced and the importance of a confined environment is explained. In Section  5, the formal definitions and explanations for resources, nodes, lifespan and capacity are given. In Section  6, a case study for DIRECT in a molecular communication nanonetwork using pulse-based modulation is analyzed. A number of tests are performed in order to observe the interdependencies between the essential parameters that define the environment, and simulation results are discussed. We conclude the paper in Section  7, where a path for future work is also given.

Section snippets

Molecular harvesting in biological systems

Calcium ions play an important role in the cell life as a fundamental second messenger in signal transduction pathways  [21]. The variations of cytosolic Ca2+ concentration are important regulatory factors for the control of cellular functions. In fact, an increase in intracellular Ca2+ concentration, in response to extracellular signals, can trigger and modulate several events, such as muscle contraction, cell growth, proliferation and many others  [9], [8], [28]. This may happen through the

State of the art

Molecular communication has been an attractive topic for researchers after the introduction of the nanoscale communications. Numerous potential applications of nanonetworks make molecular communication even more appealing. These potential applications range from biomedical applications, such as intelligent drug delivery and health monitoring systems, to military and environmental applications such as air pollution monitoring  [1].

A number of different models have been proposed to describe

Operating environments

Considering the use of discrete resources in DIRECT, operating environments (or working spaces) can be classified into three categories according to the scope of the particle movement due to the existence of the boundaries: confined, unconfined and locally unconfined (Fig. 1).

A confined operating environment (Fig. 1(a)) is a closed working environment, bounded with reflective borders. Any resource reaching to the boundaries reflects back into the environment. Thus, the number of total resources

Resources and nodes

In DIRECT, a resource is a discrete physical entity which is required by a task, such as modulation of the signal, within the network. Resources can be considered as the atomic entities within the network. They are perpetual and reusable; they do not disperse or attenuate. If proper harvesting mechanisms are applied, resources are 100% reusable. Ca2+ is an analogous example of a resource involved in molecular communication.

Nodes are autonomous agents, and they constitute the basic functional

Experiments

A set of experiments has been performed to observe the behavior of DIRECT in modeling molecular networks. Three essential parameters are investigated during experiments, and the relationship between them is studied. These parameters are:

  • (1)

    Pulse amplitude (A) is the number of resources that constitute an emitted pulse initially.

  • (2)

    Background concentration (b) is the initial concentration of resources over the operating environment.

  • (3)

    Number of nodes (n) is the total number of nodes available in the

Conclusion and future work

Molecular communication presents fundamental differences with respect to traditional wireless communications. Among these, the use of molecules as the information carrier is probably the most relevant one. As a consequence, an analytical framework that takes this unique characteristic into account is needed in order to analyze the performance of molecular communication nanonetworks.

This paper presents DIRECT, a networking model which can be used to understand the general properties of molecular

Acknowledgments

This work has been supported by the The Science Fellowships and Grant Programmes Department (BIDEB) of The Scientific and Technological Research Council of Turkey (TUBITAK).

Deniz Demiray was born in Istanbul in 1982. He graduated from Kocaeli University with a degree in Computer Engineering in 2005. He received a M.Sc. degree from Istanbul Technical University in 2008 in Computer Science. During October 2011–October 2012 he worked at Nanonetworking Center in Catalunya (N3Cat) at UPC as a visiting researcher, and joined N3Cat. He is currently pursuing a Ph.D. in Computer Science at Istanbul Technical University. His research interests are nanonetworking, molecular

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    Deniz Demiray was born in Istanbul in 1982. He graduated from Kocaeli University with a degree in Computer Engineering in 2005. He received a M.Sc. degree from Istanbul Technical University in 2008 in Computer Science. During October 2011–October 2012 he worked at Nanonetworking Center in Catalunya (N3Cat) at UPC as a visiting researcher, and joined N3Cat. He is currently pursuing a Ph.D. in Computer Science at Istanbul Technical University. His research interests are nanonetworking, molecular communication, nature inspired computing and swarm intelligence.

    Albert Cabellos-Aparicio received a B.Sc. (2001), M.Sc. (2005) and Ph.D. (2008) degree in Computer Science Engineering from the Technical University of Catalonia (www.upc.edu). In 2004 he was awarded with a full scholarship to carry out Ph.D. studies at the Department of Computer Architecture, Technical University of Catalonia (UPC), Spain. In September 2005 he became an assistant professor of the Computer Architecture Department and as a researcher in the Broadband Communications Group (http://cba.upc.edu/). In 2010 he joined the NaNoNetworking Center in Catalunya (http://www.n3cat.upc.edu) where he is the Scientific Director. He is an editor of the Elsevier Journal on Nano Computer Network and member of the Project Management Committee of the LISPmob opensource initiative (http://lispmob.org). His main research interests are future architectures for the Internet and Nanonetworks.

    Eduard Alarcón received the M.Sc. (National award) and Ph.D. degrees (honors) in Electrical Engineering from the Technical University of Catalunya (UPC BarcelonaTech), Spain, in 1995 and 2000, respectively. Since 1995 he has been with the Department of Electronic Engineering at UPC, where he became Associate Professor in 2000. He is the scientific co-director of N3CAT, the center for Nanonetworks at UPC. During the period 2006–2009 he was Associate Dean of International Affairs at the School of Telecommunications Engineering, UPC. From August 2003 to January 2004, July–August 2006 and July–August 2010 he was a Visiting Professor at the CoPEC center, University of Colorado at Boulder, USA, and during January–June 2011 he was Visiting Professor at the School of ICT/Integrated Devices and Circuits, Royal Institute of Technology (KTH), Stockholm, Sweden. He has co-authored more than 250 international scientific publications, 4 books, 4 book chapters and 4 patents, and has been involved in different National, European and US (DARPA, NSF) R&D projects within his research interests including the areas of on-chip energy management circuits, energy harvesting and wireless energy transfer, and communications at the nanoscale. He is the PI of the Guardian Angels EU FET flagship project at UPC. He has given 25 invited or plenary lectures and tutorials in Europe, America and Asia, and was appointed by the IEEE CAS society as a distinguished lecturer for 2009–2010 and lectures yearly MEAD courses at EPFL. He is elected member of the IEEE CAS Board of Governors (2010–2013) and member of the IEEE CAS long term strategy committee. He was recipient of the Myril B. Reed Best Paper Award at the 1998 IEEE Midwest Symposium on Circuits and Systems. He was the invited co-editor of a special issue of the Analog Integrated Circuits and Signal Processing journal devoted to current-mode circuit techniques, and a special issue of the International Journal on Circuit Theory and Applications. He co-organized special sessions related to on-chip power management at IEEE ISCAS03, IEEE ISCAS06 and NOLTA 2012, and lectured tutorials at IEEE ISCAS09, ESSCIRC 2011, IEEE VLSI-DAT 2012 and APCCAS 2012. He was the 2007 Chair of the IEEE Circuits and Systems Society Technical Committee of Power Systems and Power Electronics Circuits. He was the technical program co-chair of the 2007 European Conference on Circuit Theory and Design—ECCTD07 and of LASCAS 2013, Special Sessions co-chair at IEEE ISCAS 2013, tutorial co-chair at ICM 2010 and ISCAS 2013, Demo Chair of BodyNets 2012, track co-chair of the IEEE ISCAS 2007, IEEE MWSCAS07, IEEE ISCAS 2008, ECCTD’09, IEEE MWSCAS09, IEEE ICECS’2009, ESSCIRC 2010, PwrSOC 2010, IEEE MWSCAS12 and TPC member for IEEE WISES 2009, WISES 2010, IEEE COMPEL 2010, IEEE ICECS 2010, IEEE PRIME 2011, ASQED 2011, ICECS 2011, INFOCOM 2011, MoNaCom 2012, LASCAS 2012, PwrSOC 2012, ASQED 2012, IEEE PRIME 2012, IEEE iThings 2012 and CDIO 2013. He served as an Associate Editor of the IEEE Transactions on Circuits and Systems—II: Express briefs (2006–2007) and currently serves as Associate Editor of the Transactions on Circuits and Systems—I: Regular papers (2006-), Elsevier’s Nano Communication Networks journal (2009-), Journal of Low Power Electronics (JOLPE) (2011-) and in the Senior Editorial Board of the IEEE Journal on IEEE Journal on Emerging and Selected Topics in Circuits and Systems (2010-).

    D. Turgay Altilar received his Ph.D. degree in 2002 from Queen Mary, University of London. He was involved with several EU projects related to parallel multimedia processing during his Ph.D. research. He has been assigned as an Associate Professor in 2012 at the Computer Engineering Department of Istanbul Technical University. Dr. Altilar’s research interests are related to wireless sensor networks, cognitive radio, real-time systems, pervasive computing, parallel, distributed and grid computing. The current research interests are nanonetworking, routing protocol design in cognitive radio networks, data dissemination on multimedia sensor networks, MAC and routing protocol design for multichannel sensor networks, resource management Grid Computing and naturally tolerant parallel algorithm design and heterogeneous network-based GPGPU computing. He has served as technical program committee chair, technical program committee member, session and symposium organizer, and workshop chair in several conferences. Dr. Altilar is a member of IEEE.

    Ignacio Llatser was born in Vinaròs (Spain) in 1984. In 2008, he graduated with a double M.S. degree in Telecommunication Engineering and Computer Science from the Technical University of Catalonia (UPC). He completed his Master Thesis on game-theoretical protocols for vehicular networks in the Laboratory for Computer Communications and Applications, at the École Polytechnique Fédérale de Lausanne (EPFL). In 2009, he joined the Nanonetworking Center in Catalunya (N3Cat) at UPC, where he is currently pursuing a Ph.D. in Computer Architecture. His research interests lie in the fields of nanonetworks, molecular communication and graphene-enabled wireless communications.

    Luca Felicetti received the master degree in Information and Telecommunication Engineering from University of Perugia in 2011. Now, he is a Ph.D. student at the Department of Electronic and Information Engineering, University of Perugia. His current research interests focus on nano-scale networking and communications.

    Gianluca Reali has been an Associate Professor at the University of Perugia, Department of Information and Electronic Engineering (DIEI), Italy, since January 2005. He received the Ph.D. degree in Telecommunications from the University of Perugia in 1997. From 1997 to 2004 he was a researcher at DIEI. In 1999 he visited the Computer Science Department at UCLA. His research activities include resource allocation over packet networks, wireless networking, network management, and multimedia services.

    Mauro Femminella received both the master degree and the Ph.D. in Electronic Engineering from University of Perugia in 1999 and 2003, respectively. Since November 2006, he has been Assistant Professor at the Department of Electronic and Information Engineering, University of Perugia. His current research interests focus on nano-scale networking and communications, middleware platforms for multimedia services, location and navigation systems, and network and service management architectures for the future Internet.

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