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Design and Computational Analysis of Bio-Nanorobotic Structures

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Abstract

Bio-nanorobotics is a new and rapidly growing interdisciplinary field addressing the assembly, construction and utilization of biomolecular devices based on nanoscale principles and/or dimensions. A key application is for medical target identification in therapeutical diagnosis, medical therapies and minimally invasive surgery (MIS) (Calvacanti et al. in Nanotechnology 19:1–15, 2008; Requicha in Proc. IEEE Sens. 91(11):1922–1933, 2003; Hogg and Kuekes in Nanomed. Nanotechnol. Biol. Med. 2(4):239–247, 2006) Modern engineering actuation techniques inspired by nature have been successfully implemented in microrobots evolving in fluidic environments using external electromagnetic fields (Yesin et al. in Int. J. Rob. Res. 25(5–6):527–536, 2006; Mathieu et al. in IEEE Trans. Biomed. Eng. 53(2):292–299, 2006; Behkam and Sitti in J. Dyn. Syst. Meas. Control 128:36–43, 2006). On contrary, biological approach shows that flagellated propulsion mechanisms of bacteria (Martel et al. in Appl. Phys. Lett. 89:233804, 2006), peptide based nanoGripper (Sharma et al. in Int. J. Rob. Res., 2009) or magnetic stereotaxis systems (Steager et al. in Appl. Phys. Lett. 90:263901, 2006) represent a fertile territory for untethered nanoscale machines without the need of external hardware for actuation. Developing nanorobots out of proteins elements requires the merging of two fields of research approaches: the inspiration by nature and biology (“biomimetics”) and the inspiration by large scale machines and the traditional machine theory (“machine nanomimetics”).

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References

  1. Calvacanti, A., Shririnzadeh, B., Freitas, R., Hogg, T.: Nanorobot architecture for medical target identification. Nanotechnology 19, 1–15 (2008)

    Google Scholar 

  2. Requicha, A.: Nanorobots, NEMS and nanoassembly. Proc. IEEE Sens. 91(11), 1922–1933 (2003)

    Google Scholar 

  3. Hogg, T., Kuekes, P.J.: Mobile microscopic sensors for high resolution in vivo diagnostics. Nanomed. Nanotechnol. Biol. Med. 2(4), 239–247 (2006)

    Article  Google Scholar 

  4. Yesin, K.B., Vollmers, K., Nelson, B.J.: Modeling and control of unthered biomicrorobots in a fluidic environment using electromagnetic fields. Int. J. Rob. Res. 25(5–6), 527–536 (2006)

    Article  Google Scholar 

  5. Mathieu, J.-B., Beaudoin, G., Martel, S.: Method of propulsion of a ferromagnetic core in the cardiovascular system through magnetic gradients generated by an MRI system. IEEE Trans. Biomed. Eng. 53(2), 292–299 (2006)

    Article  Google Scholar 

  6. Behkam, B., Sitti, M.: Design methodology for biomimetic propulsion of miniature swimming robots. J. Dyn. Syst. Meas. Control 128, 36–43 (2006)

    Article  Google Scholar 

  7. Martel, S., Tremblay, C., Ngakeng, S., Langlois, G.: Controlled manipulation and actuation of microobjects with magnetotactic bacteria. Appl. Phys. Lett. 89, 233804 (2006)

    Article  Google Scholar 

  8. Sharma, G., Rege, K., Budil, D., Yarmush, M., Mavroidis, C.: Computational studies of protein based nanoGripper. Int. J. Rob. Res. (2009)

    Google Scholar 

  9. Steager, E., Kim, C.B., Patel, J., Bith, S., Naik, C., Reber, L., Kim, M.J.: Control of microfabricated structures powered by flagellated bacteria using phototaxis. Appl. Phys. Lett. 90, 263901 (2006)

    Article  Google Scholar 

  10. Howard, J.: Mechanics of Motor Proteins and the Cytoskeleton. Sinauer Associates, Sunderland (2001), 367 pp.

    Google Scholar 

  11. Montegano, C.D., Bachand, G.D.: Constructing nanomechanical devices powered by biomolecular motors. Nanotechnology 10, 225–331 (1999)

    Article  Google Scholar 

  12. Amos, W.B., et al.: Calcium binding proteins in a Vorticellid contractile organelle. J. Cell Sci. 190, 203–213 (1975)

    Google Scholar 

  13. Yu, H.-h., Swager, T.M.: Molecular actuators—designing actuating materials at the molecular level. IEEE J. Ocean. Eng. 29(3), 692–695 (2004)

    Article  Google Scholar 

  14. Huang, T.J., Flood, A.H., Brough, B., Liu, Y., Bonvallet, P.A., Kang, S., Chu, C.-W., Guo, T.-F., Lu, W., Yang, Y., Stoddart, J.F., Ho, C.-M.: Understanding and harnessing biomimetic molecular machines for NEMS actuation materials. IEEE Trans. Autom. Sci. Eng. 3(3), 254–259 (2006)

    Article  Google Scholar 

  15. Sauvage, J.-P., Dietrich-Buchecker, C.: Molecular Catenanes, Rotaxanes and Knots. VCH, Weinheim (1999)

    Book  Google Scholar 

  16. Huang, T.J., et al.: A nanomechanical device based on linear molecular motors. Appl. Phys. Lett. 85, 5391–5393 (2004)

    Article  Google Scholar 

  17. Mahadevan, L., Matsudaira, P.: Mobility powered by supramolecular springs and ratchets. Science 288, 95–99 (2000)

    Article  Google Scholar 

  18. Kitamura, K., Tokunaga, M., Iwane, A.H., Yanagida, Y.: A single myosin head moves along an actin filament with rectangular steps of 5.3 nm. Nature 397, 129 (1999)

    Article  Google Scholar 

  19. Shingyoji, C., Higuchi, H., Yoshimura, M., Katayama, E., Yanagida, T.: Dynein arms are oscillating force generators. Nature 393, 711–714 (1998)

    Article  Google Scholar 

  20. Block, S.M.: Kinesin what gives? Cell 93, 5–8 (1998)

    Article  Google Scholar 

  21. Knoblauch, M., Naull, G.A., Muller, T., Prufer, D., Schneider-Huther, I., et al.: ATP-independent contractile proteins from plants. Nat. Mater. 2, 600–603 (2003)

    Article  Google Scholar 

  22. Atsumi, T., McCarter, L., Ymae, Y.: Polar and lateral flagellar motors of marine Vibrio are driven by different ion-motive forces. Nature 355(6356), 182–184 (1992)

    Article  Google Scholar 

  23. Li, J., Tan, W.: A single DNA molecule nanomotor. Nano Lett. 2, 315–318 (2002)

    Article  Google Scholar 

  24. Jorgenson, W.L., Chandrasekhar, J., Madura, D., Impey, R.W.: Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926–935 (1993)

    Article  Google Scholar 

  25. Isralewitz, B., Baudry, J., Gullingsrud, J., Kosztin, D., Schulten, K.: Steered molecular dynamics investigations of protein function. J. Mol. Graph. Model 19(12), 13–25 (2001)

    Article  Google Scholar 

  26. Park, S., Khalili-Araghi, F., Tajkhorshid, E., Schulten, K.: Free energy calculation from steered molecular dynamics simulations using Jarzynski’s equality. J. Chem. Phys. 119(6), 3559–3566 (2003)

    Article  Google Scholar 

  27. Bustamante, C., Smith, S.B., Liphardt, J., Smith, D.: Single-molecule studies of DNA mechanics. Struct. Biol. 10, 279–285 (2000)

    Article  Google Scholar 

  28. Strick, T.R., Charvin, G., Dekker, N.H., Allemand, J.-F., Bensimon, D., Croquette, V.: Tracking enzymaic steps of DNA topoisomerases using single-molecule micromanipulation. C. R. Phys. 3, 595–618 (2002)

    Google Scholar 

  29. Williams, M.C., Rouzina, I.: Force spectroscopy of single DNA and RNA molecules. Curr. Opin. Struct. Biol. 12, 330–336 (2002)

    Article  Google Scholar 

  30. Sattin, B.D., Pelling, A.E., Goh, M.C.: DNA base pair resolution by single molecule force spectroscopy. Nucleic Acids Res. 32(16), 4876–4883 (2004)

    Article  Google Scholar 

  31. Essevaz-Roulet, B., Bockelmann, U., Heslot, F.: Mechanical separation of the complementary strands of DNA. Proc. Natl. Acad. Sci. USA 94, 11935–11940 (1997)

    Article  Google Scholar 

  32. Cocco, S., Monasson, R., Marko, J.F.: Force and kinetic barriers to unzipping of the DNA double helix. Proc. Natl. Acad. Sci. USA 98(1), 8608–8613 (2001)

    Article  Google Scholar 

  33. Strom, C., Nelson, P.C.: Theory of high-force DNA stretching and overstretching. Phys. Rev. 67, 051906 (2003)

    MathSciNet  Google Scholar 

  34. Noy, A., Perez, A., Lankas, F., Luque, F.J., Orozco, M.: Relative flexibility of DNA nad RNA: a molecular dynamics study. J. Mol. Biol. 343, 627–638 (2004)

    Article  Google Scholar 

  35. Granzier, H., Labeit, S.: Cardiac titin: an adjustable multi-functional spring. J. Phys. 541, 335–342 (2002)

    Article  Google Scholar 

  36. Lu, H., Schulten, K.: Steered molecular dynamics simulations of force-induced protein domain unfolding. Proteins 35, 453–463 (1999)

    Article  Google Scholar 

  37. Gao, M., Graig, D., Vogel, V., Schulten, K.: Identifying unfolding intermediates of FN-III10 by steered molecular dynamics. Matrix Biol. 232, 939–950 (2002)

    Google Scholar 

  38. Paci, E., Karplus, M.: Forced unfolding of fibronectin type 3 modules: an analysis by biased molecular dynamics simulation. J. Mol. Biol. 288, 441–459 (1999)

    Article  Google Scholar 

  39. Marszalek, P.E., Lu, H., Li, H., Carrion-Vazquez, M., Oberhauser, A.F., Schulten, K., Fernandez, J.M.: Mechanical unfolding intermediates in titin modules. Nature 402, 100–103 (1999)

    Article  Google Scholar 

  40. Vazina, A.A., Lanina, N.F., Alexeev, D.G., Bras, W., Dolbnya, I.P.: The structural principles of multidomain organization of the giant polypeptide chain of the muscle titin protein: SAXS/WAXS studies during the stretching of oriented titin fibres. J. Cell Biol. 155(2), 251–262 (2006)

    Google Scholar 

  41. Schoenauer, R., Bertoncini, P., Machaidze, G., Aebi, U., Perriard, J.-C., Hegner, M., Agarkova, I.: Myomesin is a molecular spring with adaptable elasticity. J. Mol. Biol. 349, 367–379 (2005)

    Article  Google Scholar 

  42. Gao, M., Lu, H., Schulten, K.: Simulated refolding of stretched titin immunoglobulin domain. Biophys. J. 8, 2268–2277 (2006)

    Google Scholar 

  43. Lu, H., Schulten, K.: The key event in force-induced unfolding of titin. Biophys. J. 79, 51–65 (2000)

    Article  Google Scholar 

  44. Cramer, C.J.: Essentials of Computational Chemistry, pp. 191–232. Wiley, New York (2002)

    Google Scholar 

  45. Stewart, J.J.P.: Optimization of parameters for semiempirical methods IV: extension of MNDO, AM1, and PM3 to more main group elements. J. Mol. Model. 10, 155–164 (2004)

    Article  Google Scholar 

  46. Kuhn, B., Kollman, P.A.: Binding of a diverse set of ligands to avidin and streptavidin: an accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models. J. Med. Chem. 43, 3786–3791 (2000)

    Article  Google Scholar 

  47. Liu, Y.J., Chen, X.L.: Continuum models of carbon nanotube-based composites using the boundary element method. J. Bound. Elem. 1(2), 316–335 (2003)

    MathSciNet  Google Scholar 

  48. Gao, M., Wilmanns, M.: Steered molecular dynamics study of titin I1 domain unfolding. Biophys. J. 83, 3435–3445 (2002)

    Article  Google Scholar 

  49. Trombitas, K., Gasser, M., Labeit, S., Jin, J.-P., Kellermayer, M., Helmes, M., Granzier, H.: Titin extensibility in situ: entropic elasticity of permanently folded and permanently unfolded molecular segments. J. Cell Biol. 140, 853–859 (1998)

    Article  Google Scholar 

  50. Zhang, B., Guangzhao, X., Evans, J.S.: A kinetic molecular model of the reversible unfolding and refolding of Titin under force extension. Biophys. J. 77, 1306–1315 (1999)

    Article  Google Scholar 

  51. Day, R., Bennion, B.J., Daggett, V.: Increasing temperature accelerates protein unfolding without changing the pathway of unfolding. J. Mol. Biol. 322, 189–203 (2002)

    Article  Google Scholar 

  52. Minajeva, A., Kulke, M., Fernandez, J.M., Linke, W.A.: Unfolding of titin domains explains the viscoelastic behavior of skeletal myofibrils. J. Struct. Biol. 80, 1442–1451 (2001)

    Google Scholar 

  53. Dubey, A., Sharma, G., Mavroidis, C., Tomassone, M., Nitkitczuk, K.P., Yarmush, M.L.: Computational studies of viral protein nano-actuators. J. Comput. Theor. Nanosci. 1, 18–28 (2004)

    Article  Google Scholar 

  54. Sherman, W.B., Seeman, N.C.: A precisely controlled DNA biped walking device. Nano Lett. 4(7), 1203–1207 (2004)

    Article  Google Scholar 

  55. Simmel, F.C., Yurke, B.: Using DNA to construct and power a nanoactuator. Phys. Rev. E 63, 127–132 (2001)

    Article  Google Scholar 

  56. Yan, H., Zhang, X., Shen, Z., Seeman, N.C.: A robust DNA mechanical device controlled by hybridization topology. Nature 415, 62–65 (2002)

    Article  Google Scholar 

  57. Hummer, G., Rasaiah, J.-C., Noworyta, J.P.: Water conduction through the hydrophobic channel of a carbon nanotube. Nature 414, 188–190 (2001)

    Article  Google Scholar 

  58. Joseph, S., Mashl, R.J., Jakobsson, E., Aluru, N.R.: Electrolytic transport in modified carbon nanotubes. Nano Lett. 3, 1399–1403 (2003)

    Article  Google Scholar 

  59. Wei, C., Srivastava, D.: Theory of transport of long polymer molecules through carbon nanotube channel. Phys. Rev. Lett. 91, 235901 (2002)

    Article  Google Scholar 

  60. Zheng, Q., Jiang, Q.: Multiwalled carbon nanotubes as gigahertz oscillators. Phys. Rev. Lett. 88, 045503 (2002)

    Article  Google Scholar 

  61. Fennimore, A.M., et al.: Rotational actuators based on carbon nanotubes. Nature 424, 408–410 (2003)

    Article  Google Scholar 

  62. Dong, L., Nelson, B.J., Fukuda, T., Arai, F.: Towards nanotube linear servomotors. IEEE Trans. Autom. Sci. Eng. 3(23), 228–235 (2006)

    Article  Google Scholar 

  63. Okada, T., Kaneko, T., Hatakeyama, R.: Single-stranded DNA insertion into single-walled carbon nanotubes by ion irradiation in an electrolyte plasma. Jpn. Soc. Appl. Phys. 45, 8335–8339 (2006)

    Article  Google Scholar 

  64. Gao, H., Kong, Y., Cui, D., Ozken, G.S.: Spontaneous insertion of DNA oligonucleotides into carbon nanotubes. Nano Lett. 3(4), 471–473 (2003)

    Article  Google Scholar 

  65. Steger, G.: Thermal denaturation of double-stranded nucleic acids: prediction of temperatures critical for gradient gel electrophoresis and polymerase chain reaction. Nucleic Acids Res. 22(14), 2760–2768 (1994)

    Article  Google Scholar 

  66. Williams, M.C., Wenner, J.R., Rouzina, I., Bloomfield, V.A.: Entropy and heat capacity of DNA melting from temperature dependence of single molecule stretching. Biophys. J. 80, 1932–1939 (2001)

    Article  Google Scholar 

  67. Williams, M.C., Wenner, J.R., Rouzina, I., Bloomfield, V.A.: Effect of pH on the overstretching transition of double-stranded DNA: evidence of force-induced DNA melting. Biophys. J. 80, 874–881 (2001)

    Article  Google Scholar 

  68. Balzani, V., Venturi, M., Credi, A.: Molecular Devices and Machines: A Journey into the Nanoworld. Wiley–VCH, New York–Weinheim (2003)

    Book  Google Scholar 

  69. Wenner, J.R., Williams, M.C., Rouzina, I., Bloomfield, V.A.: Salt dependence of the elasticity and overstretching transition of single DNA molecules. Biophys. J. 82, 3160–3169 (2002)

    Article  Google Scholar 

  70. Punkkinen, O., Hansen, P.L., Miao, L., Vattulainen, I.: DNA overstretching transition: ionic strength effects. Biophys. J. 89, 967–978 (2005)

    Article  Google Scholar 

  71. He, P., Li, S., Dai, L.: DNA-modified carbon nanotubes for self-assembling and biosensing applications. Synthetic Mater. 154, 17–20 (2005)

    Article  Google Scholar 

  72. Kohandel, M., Ha, B.-Y.: Thermal denaturation of double-stranded DNA: effect of base stacking. Phys. Rev. E 73, 011905 (2006)

    Article  Google Scholar 

  73. Rouzina, I., Bloomfield, V.A.: Force-induced melting of the DNA double helix 1. Thermodynamic analysis. Biophys. J. 80, 882–893 (2001)

    Article  Google Scholar 

  74. McDonald, R.J., Dragan, A.I., Kirk, W.R., Neff, K.L., Privalov, P.L., Maher, L.J.: DNA bending by charged peptides: electrophoretic and spectroscopic analyses. Biochemistry 46, 2306–2316 (2007)

    Article  Google Scholar 

  75. Bianco, A., Kostarelos, K., Prato, M.: Applications of carbon nanotubes in drug delivery. Curr. Opin. Chem. Biol. 9, 674–679 (2005)

    Article  Google Scholar 

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Hamdi, M., Ferreira, A. (2011). Design and Computational Analysis of Bio-Nanorobotic Structures. In: Design, Modeling and Characterization of Bio-Nanorobotic Systems. Springer, Dordrecht. https://doi.org/10.1007/978-90-481-3180-8_3

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