Molecular Communication Among Nanomachines

  • Barış Atakan


In this chapter, the concept of molecular communication and nanonetwork is introduced. After briefly discussing the existing and envisioned nanomachines, nanorobots, and genetically engineered machines, it is examined why these machines need to communicate and interconnect to form a nanonetwork in sophisticated nano- and biotechnology applications. Then, molecular communication paradigms (including nature-made molecular communication mechanisms), which can be used for designing nanonetworks, are introduced. These molecular communication paradigms are categorized into two main types, i.e., passive molecular communications (PMC) and active molecular communications (AMC). Finally, the organization of the book is presented to determine how PMC and AMC will be detailed in the remainder of the book.


Gene Regulatory Network Synthetic Biology Molecular Motor Acoustic Communication Intercellular Signaling 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


  1. 1.
    Abelson H et al (2000) Amorphous computing. Communications of the ACM 43.(5):74–82Google Scholar
  2. 2.
    Balzani V, Credi A, Silvi S, Venturi M (2006) Artificial nanomachines based on interlocked molecular species: recent advances. Chem Soc Rev 35:1135–1149CrossRefGoogle Scholar
  3. 3.
    Ozin GA, Manners I, Fournier-Bidoz S, Arsenault A (2005) Dream nanomachines. Adv Mater 17:3011–3018CrossRefGoogle Scholar
  4. 4.
    Roukes M (2001) Nanoelectromechanical systems face the future. Phys World 14:25–31Google Scholar
  5. 5.
    Despont M, Brugger J, Drechsler U, Dürig U, Häberle, W, Lutwyche M, Rothuizen, H, Stutz R et al (2000) VLSI-NEMS chip for parallel AFM data storage. Sens Actuators A Phys 80:100–107CrossRefGoogle Scholar
  6. 6.
    Drexler E (1992) Nanosystems: molecular machinery, manufacturing, and computation. Wiley, New YorkGoogle Scholar
  7. 7.
    Akyildiz IF, Brunetti F, Blázquez C (2008) Nanonetworks: a new communication paradigm. Comput Netw 52:2260–2279CrossRefGoogle Scholar
  8. 8.
    Whitesides GM (2001) The once and future nanomachine. Sci Am 285:70–75Google Scholar
  9. 9.
    Soong RK, Bachand D, Neves HP, Olkhovets AG, Craighead HG, Montemagno CD (2000) Powering an inorganic nanodevice with a biomolecular motor. Science 290:1555–1558CrossRefGoogle Scholar
  10. 10.
    Montemagno CD, Bachand GD (1999) Constructing nanomechanical devices powered by biomolecular motors. Nanotechnology 10:225–331CrossRefGoogle Scholar
  11. 11.
    Bachand GD, Montemagno CD (2000) Constructing organic/inorganic NEMS devices powered by biomolecular motors. Biomed Microdevices 2:179–184CrossRefGoogle Scholar
  12. 12.
    Sherman WB, Nadrian CS (2004) A precisely controlled DNA biped walking device. Nano Lett 4:1203–1207CrossRefGoogle Scholar
  13. 13.
    Yurke B, Turberfield AJ, Mills AP Jr, Simmel FC, Neumann JL (2000) A DNA-fuelled molecular machine made of DNA. Nature 406:605–608CrossRefGoogle Scholar
  14. 14.
    Gao Y, Yoshio B (2002) Nanotechnology: carbon nanothermometer containing gallium. Nature 415:599CrossRefGoogle Scholar
  15. 15.
    Fennimore AM et al (2003) Rotational actuators based on carbon nanotubes. Nature 424:408–410CrossRefGoogle Scholar
  16. 16.
    Requicha AAG, Baur C, Bugacov A, Gazen BC, Koel B, Madhukar A, Ramachandran TR, Resch R, Will P (1998) Nanorobotic assembly of two-dimensional structures. In: Proceedings of IEEE international conference on robotics and automation, pp 3368–3374Google Scholar
  17. 17.
    Sitti M, Hashimoto H (1998) Tele-nanorobotics using atomic force microscope. In: Proceedings of IEEE/RSJ international conference on intelligent robots and systems, pp 1739–1746Google Scholar
  18. 18.
    Freitas RA Jr (1999) Nanomedicine, volume I: basic capabilities. Landes Bioscience, GeorgetownGoogle Scholar
  19. 19.
    Mavroidis C, Ferreira A (2013) Nanorobotics: past, present, and future. In: Nanorobotics. Springer, New York, pp 3–27CrossRefGoogle Scholar
  20. 20.
    Fukuda T, Arai F, Dong L (2003) Assembly of nanodevices with carbon nanotubes through nanorobotic manipulation. Proc IEEE 91(11):1803–1818CrossRefGoogle Scholar
  21. 21.
    Fukuda T, Arai F, Dong L (2005) Nanorobotic systems. Int J Adv Robot Syst 2(3):264–275Google Scholar
  22. 22.
    Dubey A, Mavroidis C, Thornton A, Nikitczuk KP, Yarmush ML (2003) Viral protein linear (VPL) nano-actuators. In: Proceedings of IEEE NANO, San Francisco, CA, 12–14 Aug 2003, vol 2, pp 140–143Google Scholar
  23. 23.
    Dubey A, Sharma G, Mavroidis C, Tomassone SM, Nikitczuk KP, Yarmush ML (2004) Dynamics and kinematics of viral protein linear nano-actuators for bio-nano robotic systems. In: Proceedings of IEEE international conference of robotics and automation, New Orleans, LA, 26 April–1 May 2004, pp 1628–1633Google Scholar
  24. 24.
    Mavroidis C, Dubey A, Yarmush M (2004) Molecular machines. Ann Rev Biomed Eng 6:363–395CrossRefGoogle Scholar
  25. 25.
    Douglas SM, Bachelet I, Church GM (2012) A logic-gated nanorobot for targeted transport of molecular payloads. Science 335(6070):831–834CrossRefGoogle Scholar
  26. 26.
    Dubey A, Mavroidis C, Tomassone SM (2006) Molecular dynamic studies of viral-protein based nano-actuators. J Comput Theor Nanosci 3(6):885–897CrossRefGoogle Scholar
  27. 27.
    Sharma G, Rege K, Budil D, Yarmush M, Mavroidis C (2008) Reversible pH-controlled DNA binding peptide nano-tweezers–an in-silico study. Int J Nanomed 3(4):505–521Google Scholar
  28. 28.
    Vartholomeos P, Fruchard M, Ferreira A, Mavroidis C (2011) MRI-guided nanorobotic systems for therapeutic and diagnostic applications. Ann Rev Biomed Eng 13:157–184CrossRefGoogle Scholar
  29. 29.
    Sitti M (2009) Miniature devices: voyage of the microrobots. Nature 458:1121–1122CrossRefGoogle Scholar
  30. 30.
    Darnton N, Turner L, Breuer K, Berg HC (2004) Moving fluid with bacterial carpets. Biophys J 86(3):1863–1870CrossRefGoogle Scholar
  31. 31.
    Dreyfus R, Baudry J, Roper ML, Fermigier M, Stone HA, Bibette J (2005) Microscopic artificial swimmers. Nature 437:862–865CrossRefGoogle Scholar
  32. 32.
    Requicha AAG (2003) Nanorobots, NEMS, and nanoassembly. Proc IEEE 91(11):1922–1933CrossRefGoogle Scholar
  33. 33.
    Braitenberg V (1986) Vehicles: experiments in synthetic psychology. MIT press, CambridgeGoogle Scholar
  34. 34.
    Jacob F, Monod J (1961) Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol 3(3):318–356CrossRefGoogle Scholar
  35. 35.
    Cases I, de Lorenzo V (2010) Genetically modified organisms for the environment: stories of success and failure and what we have learned from them. Int Microbiol 8(3):213–222.Google Scholar
  36. 36.
    Antunes MS, Ha SB, Tewari-Singh N, Morey KJ, Trofka AM, Kugrens P et al (2006) A synthetic de-greening gene circuit provides a reporting system that is remotely detectable and has a reset capacity. Plant Biotechnol J 4(6):605–622CrossRefGoogle Scholar
  37. 37.
    Bowen TA, Zdunek JK, Medford JI (2008) Cultivating plant synthetic biology from systems biology. New Phytol 179(3):583–587CrossRefGoogle Scholar
  38. 38.
    Savage DF, Way J, Silver PA (2008) Defossiling fuel: how synthetic biology can transform biofuel production. ACS Chem Biol 3(1):13–16CrossRefGoogle Scholar
  39. 39.
    Purnick PE, Weiss R (2009) The second wave of synthetic biology: from modules to systems. Nature Rev Mol Cell Biol 10(6):410–422CrossRefGoogle Scholar
  40. 40.
    Andrianantoandro E, Basu S, Karig DK, Weiss R (2006) Synthetic biology: new engineering rules for an emerging discipline. Mol Syst Biol 2(1):1–14Google Scholar
  41. 41.
    Alberts B, Bray D, Lewis J, Raff M, Roberts K, Watson JD (1994) Molecular biology of the cell. Garland, New YorkGoogle Scholar
  42. 42.
    Tkačik G, Walczak AM (2011) Information transmission in genetic regulatory networks: a review. J Phys Condens Matter 23(15):153102CrossRefGoogle Scholar
  43. 43.
    Karlson P, Lüscher M (1959) ‘Pheromones’: a new term for a class of biologically active substances. Nature 183:55–56CrossRefGoogle Scholar
  44. 44.
    Shorey HH (1976) Animal communication by pheromones. Academic, New YorkGoogle Scholar
  45. 45.
    Atakan B, Akan OB, Balasubramaniam S (2012) Body area nanonetworks with molecular communications in nanomedicine. IEEE Commun Mag 50(1): 28–34CrossRefGoogle Scholar
  46. 46.
    Benenson Y, Gil B, Ben-Dor U, Adar R, Shapiro E (2004) An autonomous molecular computer for logical control of gene expression. Nature 429(6990):423–429CrossRefGoogle Scholar
  47. 47.
    Wang WD, Chen ZT, Kang BG, Li R (2008) Construction of an artificial inter-cellular communication network using the nitric oxide signaling elements in mammalian cells. Exp Cell Res 314(4):699–706CrossRefGoogle Scholar
  48. 48.
    Nakano T et al (2012) Molecular communication and networking: opportunities and challenges. IEEE Trans NanoBiosci 11(2):135–148CrossRefGoogle Scholar
  49. 49.
    Freitas RA (2005) Nanotechnology, nanomedicine and nanosurgery. Int J Surg 3(4):243–246CrossRefMathSciNetGoogle Scholar
  50. 50.
    Moritani Y, Hiyama S, Suda T (2006) Molecular communication for health care applications. In: Proceedings of pervasive computing and communications workshopsGoogle Scholar
  51. 51.
    Malak D, Akan OB (2012) Molecular communication nanonetworks inside human body. Nano Commun Netw 3(1):19–35CrossRefGoogle Scholar
  52. 52.
    Han J, Fu J, Schoch RB (2008) Molecular sieving using nanofilters: past, present and future. Lab Chip 8(1):23–33CrossRefGoogle Scholar
  53. 53.
    Ray TS (1993) An evolutionary approach to synthetic biology: Zen and the art of creating life. Artif Life 1:179–209CrossRefGoogle Scholar
  54. 54.
    Tessier D, Radu I, Filteau M (2005) Antimicrobial fabrics coated with nano-sized silver salt crystals. In: Proceedings of NSTI nanotechnology, vol 1, pp 762–764Google Scholar
  55. 55.
    Endres RG, Wingreen NS (2008) Accuracy of direct gradient sensing by single cells. Proc Natl Acad Sci 105(41):15749–15754CrossRefGoogle Scholar
  56. 56.
    LaVan DA, McGuire T, Langer R (2003) Small-scale systems for in vivo drug delivery. Nature Biotechnol 21(10):1184–1191CrossRefGoogle Scholar
  57. 57.
    Moritani Y, Hiyama S, Suda T (2006) Molecular communication among nanomachines using vesicles. In: Proceedings of NSTI nanotechnology conferenceGoogle Scholar
  58. 58.
    Langer R (2001) Drugs on target. Science 293(5527):58–59CrossRefGoogle Scholar
  59. 59.
    Hiyama S, Moritani Y, Suda T, Egashira R, Enomoto A, Moore M, Nakano T (2005) Molecular communication. In: Proceedings of NSTI nanotechnology conference, vol 3, pp 392–395Google Scholar
  60. 60.
    Nakano T, Suda T, Moore M, Egashira R, Enomoto A, Arima K (2005) Molecular communication for nanomachines using intercellular calcium signaling. In: Proceedings of IEEE conference on nanotechnology, pp 478–481Google Scholar
  61. 61.
    Nakano T, Hsu Y H, Tang W C, Suda T, Lin D, Koujin T, Hiraoka Y (2008) Microplatform for intercellular communication. In: Proceedings of IEEE international conference on nano/micro engineered and molecular systems, pp 476–479Google Scholar
  62. 62.
    Nakano T, Suda T, Koujin T, Haraguchi T, Hiraoka Y (2008) Molecular communication through gap junction channels. Trans Comput Syst Biol X 5410:81–99CrossRefGoogle Scholar
  63. 63.
    Nakano T, Koujin T, Suda T, Hiraoka Y, Haraguchi T (2009) A locally induced increase in intracellular propagates cell-to-cell in the presence of plasma membrane atpase inhibitors in non-excitable cells. FEBS Lett 583(22):3593–3599CrossRefGoogle Scholar
  64. 64.
    Moore M, Enomoto A, Nakano T, Egashira R, Suda T, Kayasuga A, Oiwa K (2006) A design of a molecular communication system for nanomachines using molecular motors. In: Proceedings of IEEE pervasive computing and communications workshopsGoogle Scholar
  65. 65.
    Enomoto A, Moore M, Nakano T, Egashira R, Suda T, Kayasuga A, Oiwa K (2006) A molecular communication system using a network of cytoskeletal filaments. In: Proceedings of NSTI nanotechnology conferenceGoogle Scholar
  66. 66.
    Hiyama S, Inoue T, Shima T, Moritani Y, Suda T, Sutoh K (2008) Autonomous loading, transport, and unloading of specified cargoes by using DNA hybridization and biological motor-based motility. Small 4(4):410–415CrossRefGoogle Scholar
  67. 67.
    Hess H, Matzke CM, Doot RK, Clemmens J, Bachand GD, Bunker BC, Vogel V (2003) Molecular shuttles operating undercover: a new photolithographic approach for the fabrication of structured surfaces supporting directed motility. Nano Lett 3(12):1651–1655CrossRefGoogle Scholar
  68. 68.
    Gregori M, Akyildiz IF (2010) A new nanonetwork architecture using flagellated bacteria and catalytic nanomotors. IEEE J Sel Areas Commun 8(4):612–619CrossRefGoogle Scholar
  69. 69.
    Cobo LC, Akyildiz IF (2010) Bacteria-based communication in nanonetworks. Nano Commun Netw 1(4):244–256CrossRefGoogle Scholar
  70. 70.
    Gregori M, Llatser I, Cabellos-Aparicio A, Alarcón E (2011) Physical channel characterization for medium-range nanonetworks using flagellated bacteria. Comput Netw 55(3):779–791CrossRefMATHGoogle Scholar
  71. 71.
    Guney A, Atakan B, Akan OB (2012) Mobile ad hoc nanonetworks with collision-based molecular communication. IEEE Trans Mobile Comput 11(3):353–366CrossRefGoogle Scholar
  72. 72.
    Hiyama S, Yuki M (2010) Molecular communication: Harnessing biochemical materials to engineer biomimetic communication systems. Nano Communication Networks 1(1): 20–30CrossRefGoogle Scholar
  73. 73.
    Teuscher C et al (2011) Challenges and promises of nano and bio communication networks. In: Proceedings of Fifth IEEE/ACM International Symposium on Networks on Chip (NoCS) pp 247–254Google Scholar

Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Barış Atakan
    • 1
  1. 1.Department of Electrical and Electronics Engineeringİzmir Institute of TechnologyUrlaTurkey

Personalised recommendations