Encyclopedia of Nanotechnology

2012 Edition
| Editors: Bharat Bhushan

Molecular Dynamics Simulations of Nano-Bio Materials

  • Melissa A. Pasquinelli
  • Yaroslava G. YinglingEmail author
Reference work entry
DOI: https://doi.org/10.1007/978-90-481-9751-4_402



Nano-bio materials are materials that are composed of biomolecules (protein, DNA, RNA, lipids) and nanoscale materials (nanoparticles, nanotubes, nanocrystals).

Molecular dynamics simulation is a computer simulation technique that is based on integration of Newton’s equations of motion and reflects physical movements of atoms and molecules.



Nanotechnology has received increasing public attention as more and more practical applications of nanoparticles and nanomaterials are emerging, especially in the biomedical field. For example, inorganic nanoparticles (NPs) functionalized with synthetic or biological molecules have been used in a broad range of biomedical applications, including imaging, diagnostics, and drug delivery. The advantage of using NPs in biomedical applications is that a single nanoparticle can simultaneously carry imaging probes, drug...

This is a preview of subscription content, log in to check access.


  1. 1.
    Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E.: The Protein Data Bank. Nucleic Acids Res. 28, 235–242 (2000)Google Scholar
  2. 2.
    Guvench, O., MacKerell Jr., A.D.: Comparison of protein force fields for molecular dynamics simulations. Methods Mol. Biol. 443, 63–88 (2008)Google Scholar
  3. 3.
    Case, D.A., Darden, T.A., Cheatham I, T.E., Simmerling, C.L., Wang, J., Duke, R.E., Luo, R., Crowley, M., Walker, R.C., Zhang, W., Merz, K.M., Wang, B., Hayik, S., Roitberg, A., Seabra, G., Kolossváry, I., Wong, K.F., Paesani, F., Vanicek, J., Wu, X., Brozell, S.R., Steinbrecher, T., Gohlke, H., Yang, L., Tan, C., Mongan, J., Hornak, V., Cui, G., Mathews, D.H., Seetin, M.G., Sagui, C., Babin, V., Kollman, P.A.: AMBER 10. University of California, San Francisco (2008)Google Scholar
  4. 4.
    MacKerell Jr., A.D., Banavali, N., Foloppe, N.: Development and current status of the CHARMM force field for nucleic acids. Biopolymers 56, 257–265 (2000)Google Scholar
  5. 5.
    MacKerell, A.D., Bashford, D., Bellott, M., Dunbrack, R.L., Evanseck, J.D., Field, M.J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F.T.K., Mattos, C., Michnick, S., Ngo, T., Nguyen, D.T., Prodhom, B., Reiher, W.E., Roux, B., Schlenkrich, M., Smith, J.C., Stote, R., Straub, J., Watanabe, M., Wiorkiewicz-Kuczera, J., Yin, D., Karplus, M.: All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 102, 3586–3616 (1998)Google Scholar
  6. 6.
    Duan, Y., Wu, C., Chowdhury, S., Lee, M.C., Xiong, G.M., Zhang, W., Yang, R., Cieplak, P., Luo, R., Lee, T., Caldwell, J., Wang, J.M., Kollman, P.: A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J. Comput. Chem. 24, 1999–2012 (2003)Google Scholar
  7. 7.
    Wang, J., Wolf, R.M., Caldwell, J.W., Kollman, P.A., Case, D.A.: Development and testing of a general amber force field. J. Comput. Chem. 25, 1157–1174 (2004)Google Scholar
  8. 8.
    Damm, W., Halgren, T.A., Murphy, R.B., Smondyrev, A.M., Friesner, R.A., Jorgensen, W.L.: OPLS_2002: a new version of the OPLS-AA force field. Abstr. Pap. Am. Chem. Soc. 224, U471–U471 (2002)Google Scholar
  9. 9.
    Christen, M., Hunenberger, P.H., Bakowies, D., Baron, R., Burgi, R., Geerke, D.P., Heinz, T.N., Kastenholz, M.A., Krautler, V., Oostenbrink, C., Peter, C., Trzesniak, D., van Gunsteren, W.F.: The GROMOS software for biomolecular simulation: GROMOS05. J. Comput. Chem. 26, 1719–1751 (2005)Google Scholar
  10. 10.
    Marrink, S.J., Risselada, H.J., Yefimov, S., Tieleman, D.P., de Vries, A.H.: The MARTINI force field: coarse grained model for biomolecular simulations. J. Phys. Chem. B 111, 7812–7824 (2007)Google Scholar
  11. 11.
    Johnson, R.R., Rego, B.J., Johnson, A.T.C., Klein, M.L.: Computational study of a nanobiosensor: a single-walled carbon nanotube functionalized with the coxsackie-adenovirus receptor. J. Phys. Chem. B 113, 11589–11593 (2009)Google Scholar
  12. 12.
    Kraszewski, S., Tarek, M., Treptow, W., Ramseyer, C.: Affinity of C-60 neat fullerenes with membrane proteins: a computational study on potassium channels. ACS Nano 4, 4158–4164 (2010)Google Scholar
  13. 13.
    Lin, J.Q., Zhang, H.W., Chen, Z., Zheng, Y.G.: Penetration of lipid membranes by gold nanoparticles: insights into cellular uptake, cytotoxicity, and their relationship. ACS Nano 4, 5421–5429 (2010)Google Scholar
  14. 14.
    Aubin-Tam, M.E., Hwang, W., Hamad-Schifferli, K.: Site-directed nanoparticle labeling of cytochrome c. Proc. Natl. Acad. Sci. USA 106, 4095–4100 (2009)Google Scholar
  15. 15.
    Lee, O.S., Schatz, G.C.: Molecular dynamics simulation of DNA-functionalized gold nanoparticles. J. Phys. Chem. C 113, 2316–2321 (2009)Google Scholar
  16. 16.
    Monticelli, L., Salonen, E., Ke, P.C., Vattulainen, I.: Effects of carbon nanoparticles on lipid membranes: a molecular simulation perspective. Soft Matter 5, 4433–4445 (2009)Google Scholar
  17. 17.
    Makarucha, A.J., Todorova, N., Yarovsky, I.: Nanomaterials in biological environment: a review of computer modelling studies. Eur. Biophys. J. Biophys. Lett. 40, 103–115 (2011)Google Scholar
  18. 18.
    Ke, P.C., Lamm, M.H.: A biophysical perspective of understanding nanoparticles at large. Phys. Chem. Chem. Phys. 13, 7273–7283 (2011)Google Scholar
  19. 19.
    Lane, J.M.D., Grest, G.S.: Spontaneous asymmetry of coated spherical nanoparticles in solution and at liquid-vapor interfaces. Phys. Rev. Lett. 10(4), 235501 (2010)Google Scholar
  20. 20.
    Ghorai, P.K., Glotzer, S.C.: Molecular dynamics simulation study of self-assembled monolayers of alkanethiol surfactants on spherical gold nanoparticles. J. Phys. Chem. C 111, 15857–15862 (2007)Google Scholar
  21. 21.
    Hung, A., Mwenifumbo, S., Mager, M., Kuna, J.J., Stellacci, F., Yarovsky, I., Stevens, M.M.: Ordering surfaces on the nanoscale: implications for protein adsorption. J. Am. Chem. Soc. 133, 1438–1450 (2011)Google Scholar
  22. 22.
    Auer, S., Trovato, A., Vendruscolo, M.: A condensation-ordering mechanism in nanoparticle-catalyzed peptide aggregation. PLoS Comput. Biol. 5, e1000458 (2009)Google Scholar
  23. 23.
    Mitchell, J.S., Laughton, C.A., Harris, S.A.: Atomistic simulations reveal bubbles, kinks and wrinkles in supercoiled DNA. Nucleic Acids Res. 39, 3928–3938 (2011)Google Scholar
  24. 24.
    Wong, K.Y., Pettitt, B.M.: A study of DNA tethered to surface by an all-atom molecular dynamics simulation. Theor. Chem. Acc. 106, 233–235 (2001)Google Scholar
  25. 25.
    Yao, L., Sullivan, J., Hower, J., He, Y., Jiang, S.: Packing structures of single-stranded DNA and double-stranded DNA thiolates on Au(111): a molecular simulation study. J. Chem. Phys. 12(7), 195101 (2007)Google Scholar
  26. 26.
    Singh, A., Snyder, S., Lee, L., Johnston, A.P.R., Caruso, F., Yingling, Y.G.: Effect of oligonucleotide length on the assembly of dna materials: molecular dynamics simulations of layer-by-layer DNA films. Langmuir 26, 17339–17347 (2010)Google Scholar
  27. 27.
    Lara, F.V., Starr, F.W.: Stability of DNA-linked nanoparticle crystals I: effect of linker sequence and length. Soft Matter 7, 2085–2093 (2011)Google Scholar

Copyright information

© Springer Science+Business Media B.V. 2012

Authors and Affiliations

  • Melissa A. Pasquinelli
    • 1
  • Yaroslava G. Yingling
    • 2
    Email author
  1. 1.Fiber and Polymer Science, Textile Engineering, Chemistry and ScienceNorth Carolina State UniversityRaleighUSA
  2. 2.Materials Science and EngineeringNorth Carolina State UniversityRaleighUSA