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Concentration-Encoded Molecular Communication in Nanonetworks. Part 1: Fundamentals, Issues, and Challenges

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Book cover Modeling, Methodologies and Tools for Molecular and Nano-scale Communications

Abstract

Concentration-encoded molecular communication (CEMC) is a technique in molecular communication (MC) paradigm where information is encoded into the amplitude of the transmission rate of molecules at the transmitting nanomachine (TN) and, correspondingly, the transmitted information is decoded by observing the concentration of information molecules at the receiving nanomachine (RN). In this chapter, we particularly focus on the fundamentals, issues, and challenges of CEMC system towards the realization of molecular nanonetworks. CEMC is a simple encoding approach in MC using a single type of information molecules only and without having to alter the internal structure of molecules, or use distinct molecules. Despite its simplicity, CEMC suffers from several challenges that need to be addressed in detail. Although there exists some literature on MC and nanonetworks in general, in this chapter, we particularly focus on CEMC system and provide a comprehensive overview of the principles, prospects, issues, and challenges of CEMC system.

This research work was completed while M.U. Mahfuz was with the University of Ottawa, Canada.

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Notes

  1. 1.

    Lysozyme is a kind of enzyme [4].

  2. 2.

    1 nm is equal to 10−9 (i.e. billionth) of a metre. It is approximately 1/80,000 of the typical diameter of a human hair, or 10 times the diameter of a hydrogen atom [13].

Abbreviations

CEMC:

Concentration-encoded molecular communication

EM:

Electromagnetic

ISI:

Intersymbol interference

LRBP:

Ligand-receptor binding process

M-AM:

Multiple amplitude modulation

MC:

Molecular communication

NEMS:

Nano-electromechanical systems

OOK:

On-off keying

PAM:

Pulse amplitude modulation

RN:

Receiving nanomachine

TN:

Transmitting nanomachine

VAI:

Vibrio fischeri Auto-Inducer

VRV:

Virtual receive volume

References

  1. Höfling F, Franosch T (2013) Anomalous transport in the crowded world of biological cells. Rep Prog Phys 76:046602

    Article  MathSciNet  Google Scholar 

  2. Metzler R, Klafter J (2000) The random walk’s guide to anomalous diffusion: a fractional dynamics approach. Phys Rep 339:1–77, 12

    Google Scholar 

  3. Einstein A (1905) On the movement of small particles suspended in stationary liquids required by the molecular-kinetic theory of heat. Ann Phys 17:549–560

    Article  Google Scholar 

  4. Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2008) Molecular biology of the cell. Garland Science, New York

    Google Scholar 

  5. Berg HC (1993) Random walks in biology. Princeton University Press, NJ, USA

    Google Scholar 

  6. Hiyama S, Moritani Y, Suda T, Egashira R, Enomoto A, Moore M, Nakano T (2005) Molecular communication. In: Proceedings of the NSTI nanotechnology conference

    Google Scholar 

  7. Feynman RP (1960) There’s Plenty of Room at the Bottom. Eng Sci, Caltech, USA:22–36

    Google Scholar 

  8. Taniguchi N (1974) On the basic concept of nanotechnology. In: Proceedings of the international conference on product engineering, Part II. Tokyo, Japan Society of Precision Engineering, pp 18–23

    Google Scholar 

  9. Freitas RA (2005) Nanotechnology, nanomedicine and nanosurgery. Int J Surg 3:243–246

    Article  Google Scholar 

  10. Akyildiz IF, Brunetti F, Blazquez C (2008) Nanonetworks: a new communication paradigm. Comput Netw J 52:2260–2279

    Article  Google Scholar 

  11. 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. Adv Mater 15:353–389

    Article  Google Scholar 

  12. Meyyappan M, Li J, Li J, Cassell A (2006) Nanotechnology: an overview and integration with MEMS. In: 19th IEEE international conference on micro electro mechanical systems (MEMS 2006). Istanbul, pp 1–3

    Google Scholar 

  13. Lacasa NR (2009) Modeling the molecular communication nanonetworks. M.Sc. thesis, The Universitat Politècnica de Catalunya (UPC), Spain

    Google Scholar 

  14. Bush SF (2010) Nanoscale communication networks. Artech House Incorporated

    Google Scholar 

  15. Nakano T, Moore M, Enomoto A, Suda T (2011) Molecular communication technology as a biological ICT. In: Sawai H (ed) Biological functions for information and communication technologies. Springer, Berlin Heidelberg, pp 49–86

    Chapter  Google Scholar 

  16. Tseng AA, Chen K, Chen CD, Ma KJ (2003) Electron beam lithography in nanoscale fabrication: recent development. IEEE Trans Electron Packag Manufact 26:141–149

    Article  Google Scholar 

  17. Wilbur JL, Kumar A, Biebuyck HA, Kim E, Whitesides GM (1996) Microcontact printing of self-assembled monolayers: applications in microfabrication. Nanotechnol 7:452–457

    Google Scholar 

  18. Qin D, Riggs BA (2012) Nanotechnology: a top–down approach

    Google Scholar 

  19. Bhushan B (ed) (2004) Springer handbook of nanotechnology. Springer, Berlin; New York

    Google Scholar 

  20. Yun YJ, Ah CS, Kim S, Yun WS, Park BC, Ha DH (2007) Manipulation of freestanding au nanogears using an atomic force microscope. Nanotechnol 18:505304

    Article  Google Scholar 

  21. Ozin GA, Manners I, Fournier-Bidoz S, Arsenault A (2005) Dream nanomachines. Adv Mater 17:3011–3018

    Google Scholar 

  22. Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2002) Molecular biology of the cell. Garland Science, New York

    Google Scholar 

  23. Freitas RA (1999) Nanomedicine, vol 1: basic capabilities. Landes Bioscience, Austin, TX

    Google Scholar 

  24. Nakano T, Moore M (2011) Molecular communication paradigm overview. JNIT: J Next Gener Inf Technol 2:9–16

    Google Scholar 

  25. Moore MJ, Enomoto A, Suda T, Nakano T, Okaie Y (2007) Molecular communication: new paradigm for communication among nano-scale biological machines. In: Bidgoli H (ed) The handbook of computer networks. Wiley

    Google Scholar 

  26. Akyildiz IF, Jornet JM, Pierobon M (2010) Propagation models for nanocommunication networks. In: Proceedings of the fourth European conference on antennas and propagation (EuCAP), pp 1–5

    Google Scholar 

  27. Suda T, Moore M, Nakano T, Egashira R, Enomoto A (2005) Exploratory research on molecular communication between nanomachines. In: Genetic and evolutionary computation conference (GECCO), Late Breaking Papers, 25–29 June, Washington, DC, USA

    Google Scholar 

  28. Nakano T, Moore MJ, Wei F, Vasilakos AV, Shuai J (2012) Molecular communication and networking: opportunities and challenges. IEEE Trans Nanobiosci 11:135–148

    Google Scholar 

  29. Hranilovic S (2005) Wireless optical communication systems. Springer, New York

    Google Scholar 

  30. Mahfuz MU, Makrakis D, Mouftah HT (2010) On the characterization of binary concentration-encoded molecular communication in nanonetworks. Nano Commun Netw J 1:289–300

    Article  Google Scholar 

  31. Moritani Y, Hiyama S, Suda T (2007) Molecular communication a biochemically-engineered communication system. In: Frontiers in the convergence of bioscience and information technologies, FBIT 2007, pp 839–844

    Google Scholar 

  32. Parcerisa Giné L, Akyildiz IF (2009) Molecular communication options for long range nanonetworks. Comput Netw 53:2753–2766

    Google Scholar 

  33. Nakano T, Suda T, Moore M, Egashira R, Enomoto A, Arima, K (2005) Molecular communication for nanomachines using intercellular calcium signaling. In: 2005 5th IEEE conference on nanotechnology, vol. 2, pp 478–481

    Google Scholar 

  34. Moritani Y, Hiyama S, Suda T (2006) Molecular communication for health care applications. In: Fourth annual IEEE international conference on pervasive computing and communications workshops (PerCom Workshops 2006), pp 5–553

    Google Scholar 

  35. Mahfuz MU, Makrakis D, Mouftah HT (2010) Characterization of molecular communication channel for nanoscale networks. In: Proceedings 3rd international conference on bio-inspired systems and signal processing (BIOSIGNALS-2010). Valencia, Spain, pp 327–332

    Google Scholar 

  36. Smith JM (2000) The concept of information in biology. Philos Sci 67:177–194

    Google Scholar 

  37. Farsad N, Eckford AW, Hiyama S, Moritani Y (2011) A simple mathematical model for information rate of active transport molecular communication. In: 2011 IEEE conference on computer communications workshops (INFOCOM WKSHPS), pp 473–478

    Google Scholar 

  38. Bossert WH, Wilson EO (1963) The analysis of olfactory communication among animals. J Theor Biol 5:443–469

    Article  Google Scholar 

  39. Atakan B, Akan OB (2010) Deterministic capacity of information flow in molecular nanonetworks. Nano Commun Netw 1:31–42

    Google Scholar 

  40. Eckford AW (2007) Achievable information rates for molecular communication with distinct molecules. In: 2nd Bio-Inspired models of network, information and computing systems, 2007 (Bionetics 2007), pp 313–315

    Google Scholar 

  41. Mahfuz MU, Makrakis D, Mouftah HT (2011) A comprehensive study of concentration-encoded unicast molecular communication with binary pulse transmission. In: 2011 11th IEEE conference on nanotechnology (IEEE-NANO), pp 227–232

    Google Scholar 

  42. Gillespie DT (2000) The chemical Langevin equation. J Chem Phys 113:297–306

    Google Scholar 

  43. Crank J (1975) The mathematics of diffusion. Clarendon Press, Oxford, Eng

    MATH  Google Scholar 

  44. Durrett R (2010) Probability: Theory and examples, 4th edn. Cambridge University Press

    Google Scholar 

  45. Krivan V, Lánský P, Rospars JP (2002) Coding of periodic pulse stimulation in chemoreceptors. BioSyst 67:121–128

    Article  Google Scholar 

  46. Rospars J, Křivan V, Lánský P (2000) Perireceptor and receptor events in olfaction. comparison of concentration and flux detectors: a modeling study. Chem Senses 25:293–311

    Article  Google Scholar 

  47. Moore MJ, Nakano T (2011) Synchronization of inhibitory molecular spike oscillators. In: BIONETICS-2011

    Google Scholar 

  48. Mosharov EV, Sulzer D (2005) Analysis of exocytotic events recorded by amperometry. Nat Methods 2:651–658

    Article  Google Scholar 

  49. Mahfuz MU, Makrakis D, Mouftah HT (2013) Sampling based optimum signal detection in concentration-encoded molecular communication receiver architecture and performance. In: Proceedings of the 6th international conference on bio-inspired systems and signal processing (BIOSIGNALS-2013). Barcelona, Spain

    Google Scholar 

  50. Nakano T, Liu Jian-Qin (2010) Design and analysis of molecular relay channels: an information theoretic approach. IEEE Trans NanoBiosci 9:213–221

    Article  Google Scholar 

  51. Kuran MS, Tugcu T, Edis BO (2012) Calcium signaling: overview and research directions of a molecular communication paradigm. IEEE Wireless Commun 19:20–27

    Article  Google Scholar 

  52. van Milligen BP, Bons PD, Carreras BA, Sánchez R (2005) On the applicability of Fick’s law to diffusion in inhomogeneous systems. Eur J Phys 26:913–925

    Google Scholar 

  53. Mahfuz MU, Makrakis D, Mouftah HT (2011) Characterization of intersymbol interference in concentration-encoded unicast molecular communication. In: 2011 24th Canadian conference on electrical and computer engineering (CCECE), pp 000164–000168

    Google Scholar 

  54. Pierobon M, Akyildiz IF (2012) Intersymbol and co-channel interference in diffusion-based molecular communication. In: 2012 IEEE international conference on communications (ICC), pp 6126-6131

    Google Scholar 

  55. Kuran MŞ, Yilmaz HB, Tugcu T, Akyildiz IF (2012) Interference effects on modulation techniques in diffusion based nanonetworks. Nano Commun Netw 3:65–73, 201203

    Google Scholar 

  56. Kuran MS, Tugcu T (2011) Co-channel interference for communication via diffusion system in molecular communication. In: BIONETICS 2011, York, UK, pp 199–212

    Google Scholar 

  57. Kuran MS, Yilmaz HB, Tugcu T, Akyildiz IF (2011) Modulation techniques for communication via diffusion in nanonetworks. In: 2011 IEEE international conference on communications (ICC), pp 1–5

    Google Scholar 

  58. Noel A, Cheung KC, Schober R (2013) Improving receiver performance of diffusive molecular communication with enzymes, pp 1–12. arXiv:1305.1926

  59. Noel A, Cheung KC, Schober R (2012) Improving diffusion-based molecular communication with unanchored enzymes. In: Proceedings of the 7th international conference on bio-inspired models of network, information, and computing systems (BIONETICS 2012), December

    Google Scholar 

  60. Mahfuz MU, Makrakis D, Mouftah HT (2013) A generalized strength-based signal detection model for concentration-encoded molecular communication. In: Proceedings of the 8th international conference on body area networks (BodyNets 2013). Boston, MA, USA (30 Sept.-02 Oct., 2013), pp 461–467

    Google Scholar 

  61. Mahfuz MU, Makrakis D, Mouftah HT (2011) On the characteristics of concentration-encoded multi-level amplitude modulated unicast molecular communication. In: 2011 24th Canadian conference on electrical and computer engineering (CCECE), pp 000312–000316

    Google Scholar 

  62. Mahfuz MU, Makrakis D, Mouftah H (2010) Spatiotemporal distribution and modulation schemes for concentration-encoded medium-to-long range molecular communication. In: 2010 25th Biennial symposium on communications (QBSC), pp 100–105

    Google Scholar 

  63. Moore MJ, Suda T, Oiwa K (2009) Molecular communication: modeling noise effects on information rate. IEEE Trans NanoBiosci 8:169–180

    Google Scholar 

  64. Mahfuz MU, Makrakis D, Mouftah HT (2013) Concentration encoded molecular communication: prospects and challenges towards nanoscale networks. In: Proceedings of international conference on engineering, research, innovation and education (ICERIE-2013). Sylhet, Bangladesh pp 508–513

    Google Scholar 

  65. Nakano T, Shuai J (2011) Repeater design and modeling for molecular communication networks. In: 2011 IEEE conference on computer communications workshops (INFOCOM WKSHPS), pp 501–506

    Google Scholar 

  66. Garralda N, Llatser I, Cabellos-Aparicio A, Pierobon M (2011) Simulation-based evaluation of the diffusion-based physical channel in molecular nanonetworks. In: 2011 IEEE conference on computer communications workshops (INFOCOM WKSHPS), pp 443–448

    Google Scholar 

  67. Garralda N, Llatser I, Cabellos-Aparicio A, Alarcón E, Pierobon M (2011) Diffusion-based physical channel identification in molecular nanonetworks. Nano Commun Netw 2:196–204, 201112

    Google Scholar 

  68. Llatser I, Pascual I, Garralda N, Cabellos-Aparicio A, Pierobon M, Alarcon E, Sole-Pareta J (2011) Exploring the physical channel of diffusion-based molecular communication by simulation. In: 2011 IEEE global telecommunications conference (GLOBECOM 2011), pp 1–5

    Google Scholar 

  69. Mahfuz MU, Makrakis D, Mouftah HT (2011) Transient characterization of concentration-encoded molecular communication with sinusoidal stimulation. In: Proceedings of the 4th international symposium on applied sciences in biomedical and communication technologies (ISABEL’11), Article 14, 6 Pages. Barcelona, Spain

    Google Scholar 

  70. Moore MJ, Nakano T (2011) Addressing by beacon distances using molecular communication. Nano Commun Netw J 2:161–173

    Article  Google Scholar 

  71. Mahfuz MU, Makrakis D, Mouftah HT (2011) On the detection of binary concentration-encoded unicast molecular communication in nanonetworks. In: Proceedings 4th international conference on bio-inspired systems and signal processing (BIOSIGNALS-2011), 26–29 January. Rome, Italy, pp 446–449

    Google Scholar 

  72. Mahfuz MU, Makrakis D, Mouftah HT (2012) Strength based receiver architecture and communication range and rate dependent signal detection characteristics of concentration encoded molecular communication. In: Proceedings BWCCA-2012. Victoria, Canada, pp 28–35

    Google Scholar 

  73. Mahfuz MU, Makrakis D, Mouftah HT (2013) Performance analysis of convolutional coding techniques in diffusion-based concentration-encoded PAM molecular communication systems. BioNanoSci 3:270–284

    Article  Google Scholar 

  74. Yeh PC, Chen KC, Lee YC, Meng LS, Shih PJ, Ko PY, Lin WA, Lee CH (2012) A new frontier of wireless communication theory: diffusion-based molecular communications. IEEE Wireless Commun 19:28–35

    Google Scholar 

  75. ShihP-J, Lee C-H, Yeh P-C (2012) Channel codes for mitigating intersymbol interference in diffusion-based molecular communications. In: 2012 IEEE global communications conference (GLOBECOM), pp 4228–4232

    Google Scholar 

  76. Ko P-Y, Lee Y-C, Yeh P-C, Lee C-H, Chen K-C (2012) A new paradigm for channel coding in diffusion-based molecular communications: molecular coding distance function. In: 2012 IEEE global communications conference (GLOBECOM), pp 3748–3753

    Google Scholar 

  77. Kadloor S, Adve RS, Eckford AW (2012) Molecular communication using brownian motion with drift. IEEE Trans NanoBiosci 11:89–99

    Article  Google Scholar 

  78. Srinivas K, Adve R, Eckford A (2012) Molecular communication in fluid media: the additive inverse gaussian noise channel. IEEE Trans Inf Theory 58:1

    Google Scholar 

  79. Nakano T, Okaie Y, Liu Jian-Qin (2012) Channel model and capacity analysis of molecular communication with brownian motion. IEEE Commun Lett 16:797–800

    Article  Google Scholar 

  80. Eckford AW (2007) Nanoscale communication with brownian motion. In: 2007. CISS’07. 41st annual conference on information sciences and systems, pp 160–165

    Google Scholar 

  81. Balasubramaniam S, Ben-Yehuda S, Pautot S, Jesorka A, Lio P, Koucheryavy Y (2013) A review of experimental opportunities for molecular communication. Nano Commun Netw 4:43–52

    Google Scholar 

  82. Mahfuz MU (2012) Nanoscale communication systems and their role in an emerging society. Mini-course lecture slides, University of Ottawa

    Google Scholar 

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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 2010–2013.

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Correspondence to Mohammad Upal Mahfuz .

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Mahfuz, M.U., Makrakis, D., Mouftah, H.T. (2017). Concentration-Encoded Molecular Communication in Nanonetworks. Part 1: Fundamentals, Issues, and Challenges. In: Suzuki, J., Nakano, T., Moore, M. (eds) Modeling, Methodologies and Tools for Molecular and Nano-scale Communications. Modeling and Optimization in Science and Technologies, vol 9. Springer, Cham. https://doi.org/10.1007/978-3-319-50688-3_1

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