Concentration Encoded Molecular Communication: Prospects and Challenges Towards Nanoscale Networks

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1 508 M a h f u z. e t. a l., I C E R I E Proceedings of the International Conference on Engineering Research, Innovation and Education 2013 ICERIE 2013, January, SUST, Sylhet, Bangladesh Concentration Encoded Molecular Communication: Prospects and Challenges Towards Nanoscale Networks Mohammad U. Mahfuz *, Dimitrios Makrakis, and Hussein T. Mouftah School of Electrical Engineering and Computer Science, University of Ottawa 800 King Edward Ave., Ottawa, Ontario, Canada K1N 6N5. Keywords: Nanoscale communication, Molecular communication, Concentration encoding, Nanonetworks, Nanomachines Abstract: Molecular communication (MC) is a new, bio-inspired communication paradigm towards realizing the communication and networking at the nanoscale to microscale dimensions among a vast number of engineered natural and/or artificial communicating nanomachines that form nanoscale communication networks, also known as nanonetworks. In this paper we focus on concentration-encoded molecular communication (CEMC) system where the transmitting nanomachine (TN) and the receiving nanomachine (RN) communicate with a single type of information molecules by modulating the transmission rate of information molecules at the TN. The information molecules undergo ideal (free) diffusion in three dimensions and become available to the RN that observes the concentration of the received molecules at its receptors and thus decodes the message. We provide an overview of the prospects and challenges of CEMC based nanonetworks. 1. INTRODUCTION Recently nanotechnology has revolutionized almost all disciplines of science and engineering, ranging from the physics and biology through material science to communication engineering and computer networks. With the help of the tools of nanotechnology it is now anticipated that it would become possible to build communication networks at nanoscale dimensions (Akyildiz et al. 2008, Nakano et al. 2012). The present day manufacturing technologies limit us in the fabrication of man-made nanomachines. Nanomachines are machines with at least one dimension in the range from 1 nm to 100 nm (Xia et al. 2003). 1 nm is a billion-th (i.e ) of a metre. While a single nanomachine has a very limited capability of performing simple sensing and actuation tasks that require forces in pico-newton (pn) scale a huge collection of nanomachines would be able to perform complex tasks that would handle large forces of the order of several newtons (N). As nanoscale devices are being manufactured in more and more quantities communication among such nanoscale devices would be necessary. The communication among nanomachines can be realized in four possible ways: electromagtic (EM) communication uses EM waves to communicate between nanomachines and the integration of the transmitter and the receiver at nanoscale would be difficult if not impossible. On the other hand, using acoustic waves to communicate between nanomachines requires that the acoustic transmitter and the receiver be implemented at the nanoscale, which is also a difficult task. Communication based on mechanical components e.g. joints and hinges is not feasible enough because there may not always be the mechanical contact points between the TN and the RN. Molecular communication (MC) relies on communication by using molecules between the TN and the RN. In fact MC uses one or more of the characteristics of the molecules in order to encode information to be transmitted from the TN to the RN. For example, in concentration-encoded molecular communication (CEMC) when the TN wants to transmit information bit 0 it sends a small number of molecules in the propagation medium and alternatively, when it wants to transmit a 1 it sends a large number of molecules in the medium (Mahfuz et al. 2010, Mahfuz et al. 2012). In molecular encoding the TN sends different types of molecules depending on whether it wants to send a bit 0 or 1 (Moore et al. 2009). In transmit time encoding the TN delays the transmission of the molecules when it wants to transmit a 0 or a 1 * Corresponding Author: mmahf050@uottawa.ca

2 509 M a h f u z. e t. a l., I C E R I E (Kadloor et al. 2012, Srinivas et al. 2012). Finally, information can also be encoded in the transmission order of the molecules maintained by the TN (Atakan et al. 2012). However, in this paper we consider the concentrationencoding only. The main contribution of this paper is two-fold: first, we provide a general idea of the CEMC system in diffusion based MC between nanomachines, and second, we provide an overview of the prospects and challenges of CEMC system towards the realization of nanonetworks. The paper is organized as follows: Section 2 describes the CEMC system briefly, which is followed by Section 3 discussing the opportunities of communication and networking with CEMC system in detail. Finally, Section 4 concludes the paper with possible applications of CEMC based nanonetworks to our emerging society. 2. CEMC SYSTEM As shown in Fig. 1 a unicast CEMC system consists of a pair of nanomachines called the TN and the RN. The TN transmits information molecules at a rate that is modulated with a specified modulation scheme in accordance with the information bits. A CEMC system also has information molecules e.g. proteins and ions that contain information to be transmitted, propagation medium (a.k.a. the channel ) through which the information molecules propagate and eventually reach the RN (Mahfuz et al. 2010). The RN can sense the presence of information molecules and react to them when their concentration is above or between one or more concentration thresholds. Propagation of information molecules can take place in two main ways: with active transportation, e.g. with molecular motors kinesin, dynein (Eckford et al. 2010), or passive transportation known as diffusion (Bossert and Wilson 1963, Berg 1993). In diffusion the information molecules propagate through the medium as a result of an enormous number of collisions with the solvent molecules in random-walk motion due to the thermal energy received from the environment. In this paper we consider a diffusion based propagation channel for the CEMC system between a pair of nanomachines for information communication purposes. CEMC is a five-phase communication mechanism. Encoding is the first phase when the TN translates the information into the information molecules for the transmission purposes. In CEMC information is encoded on the number of information molecules received by the RN per unit volume of the solvent molecules used. CEMC is relatively simple without having to alter the internal structure of the information molecules or send distinct molecules for information communication. In the sending phase the TN sends the encoded information molecules in the propagation medium. In the propagation phase the information molecules thus sent by the TN diffuse in the environment due to Brownian motion and become available to RN probabilistically for it to decode the message. Diffusion of information molecules depends on several factors, e.g. the size and molecular weight of the molecules, structural characteristics of the propagation medium e.g. viscosity, flow of the medium, pressure, dispersion, and absolute temperature (Berg 1993, Lacasa 2009). In the reception phase the RN senses the information molecules with its receptors located on its surface and thus detects the transmitted information symbols. Finally, in the reaction (effects) phase the RN generates any reaction or effects after decoding the received information molecules. Assuming that TN is a point source type molecular transmitter located at (0,0,0) that transmits molecules at the rate Qt () in molecules/second unit, the mean concentration U( r, t) of available information molecules at the location of the RN in molecules per unit volume at a three-dimensional space r iˆ x ˆj y kˆ z and at time t changes with time and space as 2 t Q() t r (1) U r, t exp dt Dt 4 Dt2 where r iˆ x ˆj y kˆ z is the vector indicating the distance between the TN and the RN in m, iˆ, ˆj, k ˆ are unit vectors respectively in x, y, and z dimensions when a Cartesian coordinate system is assumed, r x y z, and D is the diffusion constant of information molecules in the propagation medium in m 2 /second unit. In CEMC it is possible to use amplitude shift keying (ASK) and frequency shift keying (FSK) modulation schemes by modulating the transmission rate of the molecules at the TN. A discussion on the possible modulation schemes can be found in our earlier works (Mahfuz et al. 2010, Mahfuz et al. 2011, Mahfuz et al. 2011b). In the unicast CEMC system it is assumed that there exists time synchronization between the TN and the RN and that the TN communicates with the RN with a single type of information molecules only. Furthermore, it is assumed that the diffusion constant remains unchanged during the entire observation time and that ligand-receptor binding process (LRBP) is not considered. Here U( r, t) denotes the concentration signal intensity and can be expressed as the number of molecules that are available for reception at the location of the RN at any time instant t.

3 510 M a h f u z. e t. a l., I C E R I E Information (message) Modulation, Sending Propagation medium (Channel) Demodulator Reaction/Effect TN side RN side TN RN r 0 t 0 Diffusion of information molecules U( r, t) Fig. 1. A CEMC channel between a TN and an RN in three dimensions (adapted from Mahfuz et al. 2011c). U(r,t) molecules/cm ON-OFF modulation Time (sec.) Q(t) U(r,t) at r=800 nm U(r,t) at r=30 m Fig. 2. The input and the output signals of binary CEMC signaling when the duration of each bit is 100 seconds and the propagation medium is water. 3. PROSPECTS AND CHALLENGES OF CEMC SYSTEM 3.1 Concentration Attenuation The attenuation of concentration of available molecules at the location of the RN is one major challenge in CEMC system. The concentration of molecules gets attenuated when the communication range, i.e. the distance between the TN and the RN, increases. As a result, it is necessary to have signal amplification techniques in place in order to amplify the concentration of molecules and such that the RN can receive a reasonably acceptable concentration of the molecules at its receptors. Existing research suggest that it is possible to have signal repeaters in between the TN and the RN such that the concentration of molecules can be amplified at the destination of the signal (Nakano and Jianwei Shuai 2011). 3.2 Intersymbol Interference As shown in Fig. 3 the energy-normalized channel impulse response (CIR) suffers from temporal spreading meaning that the CIR is spread in time (Mahfuz et al. 2010). Energy-normalization of the CIR is performed by normalizing the CIR to the total energy (i.e. number of molecules) received over the entire observation time. The temporal spreading of the CIR as shown in Fig. 3 causes the output concentration signal to suffer from intersymbol interference (ISI) in the current symbol due to the residual molecules received from the previous symbol

4 Energy-normalized CIR 511 M a h f u z. e t. a l., I C E R I E transmissions. As the RN moves farther from the TN more energy interferes with the current symbol detection and thereby causing more ISI in the current symbol. ISI impacts the signal detection process significantly and so decreases the effective communication range of successful communication. This necessitates that ISI should be taken care of properly in order to ensure a reliable CEMC between nanomachines nm 15 m 30 m Time (sec.) Fig. 3. Energy-normalized CIR when the RN is at 800 nm, 15 m, and 30 m from the TN in water medium (D=10-6 cm 2 /second). 3.3 Determination of Communication Ranges In CEMC the determination of appropriate communication ranges for reliable communication is a challenge that needs to be addressed. It is found that in most cases the communication ranges depend on the characteristics of the diffusion mechanisms, which mean that communication ranges would vary for a type of information molecules in a propagation environment. Therefore, in general what would be the approximate communication ranges for reliable CEMC needs to be found. For example, our recent work has identified that for small information molecules in water medium, CEMC would be classified as short-range, medium-range, and long-range, based on whether the RN is located at <800 nm, 800 nm to 10 m, and >10 m from the TN respectively (Mahfuz et al. 2010). Since water is considered as a biologically suitable propagation environment it has been considered here in order to determine the communication ranges. Examples of other propagation media useful for CEMC and nanonetworks are air and blood plasma. 3.4 Determination of Transmission Data Rates Determination of the most suitable transmission data rate is one important challenge in CEMC. Until now it is not clearly known which of the input transmission data rates would be suitable in order to ensure reliable CEMC among nanomachines. Data rate in the range from 0.01 bits per second (bps) to 1 bps have found to be reasonably acceptable through using ASK and FSK based modulation schemes (Mahfuz et al. 2011). Since nanomachines are thought of very small capabilities it may not be suitable to use higher transmission data rates at the TN because in such cases the RN at the other side may not be able to decode the message if the transmission data rate is high enough for it. 3.5 Addressing Addressing is another important issue that has to be addressed properly in the realization of nanonetworks based on CEMC. Addressing is a technique used by a TN to selectively communicate with an RN. One of the available addressing schemes is based on concentration dependent manner, i.e. a TN can selectively choose which of the RNs it would like to communicate with by varying the number of transmitted molecules. In this way the desired RN would be able to communicate with the TN when the concentration of molecules available at that particular RN

5 512 M a h f u z. e t. a l., I C E R I E would be higher than a given concentration threshold (or within a given range of concentration thresholds) and all other RNs would not be able to communicate with the TN. The research of CEMC based nanonetworks is in its infancy and so a sufficient amount research on the issue of addressing of nanomachines in CEMC based nanonetworks is necessary. 3.6 Improvement in Communication Range and Transmission Data Rate In MC the molecules propagate in the environment between the TN and the RN and their speed of propagation is low due to the enormous number of collisions with the solvent molecules. These collisions cause random-walk based propagation and, as a result, makes MC a slow communication process. This necessitates that the communication range and transmission data rate be improved. In line with this thought it has been shown that multilevel amplitude modulation is possible in CEMC by increasing the size of the symbol alphabet (Mahfuz et al. 2011c). In addition, reducing the pulse width in on-off keying (OOK) based modulation can also be used to improve the effects of ISI and, therefore, to increase effective communication ranges (Mahfuz et al. 2011a). 3.7 Symbol Detection Methods Selection of the correct symbol detection offers a significant amount of challenge in a CEMC link between nanomachines. It is also expected that the detection challenge would be even more severe in the case of a CEMC based nanonetwork that has a huge number of communicating nanomachines working simultaneously. However, two possible detection schemes, namely sampling-based detection (SD) and energy-based detection (ED), have been proposed in the literature (Mahfuz et al. 2010). In the SD approach the RN determines the communication symbol by relying on one or more sample values of the concentration intensity U( r, t ), whereas in the ED approach the RN determines the communication symbol by comparing the accumulated number of molecules available at the RN during the entire symbol duration with a threshold. 3.8 System Model and Performance Evaluation The concepts of both MC and CEMC are very new and so the amount of available knowledge in these fields is still in the early stage. Appropriate metrics for evaluating the CEMC system need to be identified and their influence in the analysis of the system needs to be explored. Efficient amplitude modulation and frequency modulation methods need to be explored and their suitability to CEMC, based on a rigorous performance evaluation, needs to be investigated. Some works have already been done by the research community by now; however, there are several research questions that need to be answered completely in order to understand the CEMC system properly. 3.9 Test-bed Development In addition to theoretical studies experimental studies are very important in order to make a complete analysis of the CEMC system. For this reason and in order to check the suitability of CEMC to potential nanonetworks applications test-beds need to be developed by using engineered biological cells and/or artificially created cell-like structures (Nakano et al. 2011). As research progresses engineered biological nanomachines may have a bright possibility to enable CEMC based nanonetworks and provide reliable communication networks at the nanoscale. 4. CONCLUSIONS Our research shows that there is a possibility of realizing complex modulation methods, combating the ISI, determining the effective communication ranges based on available signal concentration, and developing signal detection schemes in CEMC system. We also found that the performance of a CEMC system is significantly influenced by communication ranges, transmission data rates, ISI, and detection schemes. There are several open research issues that need to be addressed in order to ensure a reliable CEMC system and develop potential applications in cancer detection, targeted drug delivery, and environmental protection and pollution control. Due to the very nature of this field a truly interdisciplinary research approach is necessary in order to realize communication and networking at the nanoscale based on CEMC.

6 513 M a h f u z. e t. a l., I C E R I E ACKNOWLEDGEMENTS M.U. Mahfuz would like to thank the Natural Sciences and Engineering Research Council of Canada (NSERC) for the financial support in the form of PGS-D scholarship during the years 2010 to REFERENCES Akyildiz, I.F., Brunetti, F. & Blazquez, C. 2008, "Nanonetworks: A New Communication Paradigm", Computer Networks Journal (Elsevier), vol. 52, pp Atakan, B., Galmes, S. & Akan, O. 2012, "Nanoscale Communication With Molecular Arrays in Nanonetworks", NanoBioscience, IEEE Transactions on, vol. PP, no. 99, pp Berg, H.C. 1993, Random Walks in Biology, Princeton University Press, NJ, USA.. Bossert, W.H. & Wilson, E.O. 1963, "The analysis of olfactory communication among animals", Journal of theoretical biology, vol. 5, no. 3, pp Eckford, A.W., Farsad, N., Hiyama, S. & Moritani, Y. 2010, "Microchannel molecular communication with nanoscale carriers: Brownian motion versus active transport", Proc. of IEEE NANO, 2010, pp Kadloor, S., Adve, R.S. & Eckford, A.W. 2012, "Molecular Communication Using Brownian Motion With Drift", NanoBioscience, IEEE Transactions on, vol. 11, no. 2, pp Lacasa, N.R. 2009, Modeling the Molecular Communication Nanonetworks, M.Sc. thesis, The Universitat Politècnica de Catalunya (UPC), Spain. Mahfuz, M.U., Makrakis, D. & Mouftah, H.T. 2012, "Communication at the Nanoscale: Prospects and Challenges of Concentration-Encoded Molecular Communication", WiSense Workshop (Poster Presentations). Mahfuz, M.U., Makrakis, D. & Mouftah, H.T. 2011, "Transient characterization of concentration-encoded molecular communication with sinusoidal stimulation", Proceedings of the 4th International Symposium on Applied Sciences in Biomedical and Communication Technologies (ISABEL '11). ACM, NY, USA,, Article 14, 6 pages. Mahfuz, M.U., Makrakis, D. & Mouftah, H.T. 2010, "Characterization of Molecular Communication Channel for Nanoscale Networks", Proc. 3rd International Conference on Bio-inspired Systems and Signal Processing (BIOSIGNALS-2010), pp Mahfuz, M.U., Makrakis, D. & Mouftah, H.T. 2011a, "Characterization of intersymbol interference in concentration-encoded unicast molecular communication", Electrical and Computer Engineering (CCECE), th Canadian Conference on, pp Mahfuz, M.U., Makrakis, D. & Mouftah, H.T. 2011b, "A comprehensive study of concentration-encoded unicast molecular communication with binary pulse transmission", Nanotechnology (IEEE-NANO), th IEEE Conference on, pp Mahfuz, M.U., Makrakis, D. & Mouftah, H.T. 2011c, "On the characteristics of concentration-encoded multi-level amplitude modulated unicast molecular communication", Electrical and Computer Engineering (CCECE), th Canadian Conference on, pp Mahfuz, M.U., Makrakis, D. & Mouftah, H.T. 2010, "On the characterization of binary concentration-encoded molecular communication in nanonetworks", Nano Communication Networks, vol. 1, no. 4, pp Moore, M.-., Suda, T. & Oiwa, K. 2009, "Molecular Communication: Modeling Noise Effects on Information Rate", NanoBioscience, IEEE Transactions on, vol. 8, no. 2, pp Nakano, T., Moore, M., Enomoto, A. & Suda, T. 2011, "Molecular Communication Technology as a Biological ICT" in Biological Functions for Information and Communication Technologies, ed. H. Sawai, Springer-Verlag, Berlin Heidelberg, pp Nakano, T. & Jianwei Shuai 2011, "Repeater design and modeling for molecular communication networks", Computer Communications Workshops (INFOCOM WKSHPS), 2011 IEEE Conference on, pp Nakano, T., Moore, M.J., Fang Wei, Vasilakos, A.V. & Jianwei Shuai 2012, "Molecular Communication and Networking: Opportunities and Challenges", NanoBioscience, IEEE Transactions on, 11(2), pp Srinivas, K., Adve, R. & Eckford, A. 2012, "Molecular Communication in Fluid Media: The Additive Inverse Gaussian Noise Channel", Information Theory, IEEE Transactions on, vol. PP, no. 99, pp Xia, Y., Yang, P., Sun, Y., Wu, Y., Mayers, B., Gates, B., Yin, Y., Kim, F. & Yan, H. 2003, "One-Dimensional Nanostructures: Synthesis, Characterization, and Applications", Advanced Materials, vol. 15, no. 5, pp