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Multiscale Modeling of Biological Protein Materials – Deformation and Failure

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Trends in Computational Nanomechanics

Abstract

Multi-scale properties of biological protein materials have been the focal point of extensive investigations over the past decades, leading to formation of a research field that connects biology and materials science, referred to as materiomics. In this chapter we review atomistic based modeling approaches applied to study the scale-dependent mechanical behavior of biological protein materials, focused on mechanical deformation and failure properties. Specific examples are provided to illustrate the application of numerical methods that link atomistic to mesoscopic and larger continuum scales. The discussion includes the formulation of atomistic simulation methods, as well as examples that demonstrate their application in case studies focused on size effects of the fracture behavior of protein materials. The link of atomistic scale features of molecular structures to structural scales at length-scales of micrometers will be discussed in the analysis of the mechanics of a simple model of the nuclear lamin network, revealing how protein networks with structural flaws cope with mechanical load

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References

  1. Alberts, B., et al., Molecular Biology of the Cell. 2002, New York: Taylor & Francis.

    Google Scholar 

  2. Astbury, W.T. and A. Street, X-ray studies of the structures of hair, wool and related fibres. I. General. Transactions of the Royal Society of London A, 1931. 230: 75–101.

    Article  Google Scholar 

  3. Weiner, S. and H.D. Wagner, The material bone: Structure mechanical function relations. Annual Review of Materials Science, 1998. 28: 271–298.

    Article  CAS  Google Scholar 

  4. Currey, J.D., Bones: Structure and Mechanics. 2002, Princeton, NJ: Princeton University Press.

    Google Scholar 

  5. Lakes, R., Materials with structural hierarchy. Nature, 1993. 361(6412): 511–515.

    Article  Google Scholar 

  6. Wegst, U.G.K. and M.F. Ashby, The mechanical efficiency of natural materials. Philosophical Magazine, 2004. 84(21): 2167–2181.

    Article  CAS  Google Scholar 

  7. Vincent, J.F.V., Structural Biomaterials, Edited by Anonymous. 1990, Princeton, NJ: Princeton University Press, p. 244.

    Google Scholar 

  8. Fratzl, P. and R. Weinkamer, Nature’s hierarchical materials. Progress in Materials Science, 2007. 52(8): 1263–1334.

    Article  CAS  Google Scholar 

  9. Aizenberg, J., et al., Skeleton of Euplectella sp.: Structural hierarchy from the nanoscale to the macroscale. Science, 2005. 309(5732): 275–278.

    Article  CAS  Google Scholar 

  10. Courtney, T.H., Mechanical Behavior of Materials. 1990, New York, USA: McGraw-Hill.

    Google Scholar 

  11. Broberg, K.B., Cracks and Fracture. 1990, London: Academic Press.

    Google Scholar 

  12. Hirth, J.P. and J. Lothe, Theory of Dislocations. 1982, New York: Wiley-Interscience.

    Google Scholar 

  13. Fraser, P. and Bickmore, W., Nuclear organization of the genome and the potential for gene regulation. Nature, 2007. 447(7143): 413–417.

    Article  CAS  Google Scholar 

  14. Engler, A.J., et al., Matrix elasticity directs stem cell lineage specification. Cell, 2006. 126(4): 677–689.

    Article  CAS  Google Scholar 

  15. Buehler, M.J., Atomistic and continuum modeling of mechanical properties of collagen: Elasticity, fracture and self-assembly. Journal of Materials Research, 2006. 21(8): 1947–1961.

    Article  CAS  Google Scholar 

  16. Buehler, M.J., Nature designs tough collagen: Explaining the nanostructure of collagen fibrils. Proceedings of the National Academy of Sciences of the United States of America, 2006. 103(33): 12285–12290.

    Article  CAS  Google Scholar 

  17. Fratzl, P., et al., Structure and mechanical quality of the collagen-mineral nano-composite in bone. Journal of Materials Chemistry, 2004. 14: 2115–2123.

    Article  CAS  Google Scholar 

  18. An, K.N., Y.L. Sun, and Z.P. Luo, Flexibility of type I collagen and mechanical property of connective tissue. Biorheology, 2004. 41(3–4): 239–246.

    CAS  Google Scholar 

  19. Ramachandran, G.N. and G. Kartha, Structure of collagen. Nature, 1955. 176: 593–595.

    Article  CAS  Google Scholar 

  20. Doyle, J., Rules of engagement. Nature, 2007. 446: 860.

    Article  CAS  Google Scholar 

  21. Kitano, H., Computational systems biology. Nature, 2002. 420(6912): 206–210.

    Article  CAS  Google Scholar 

  22. Kitano, H., Systems biology: A brief overview. Science, 2002. 295(5560): 1662–1664.

    Article  CAS  Google Scholar 

  23. Gautieri, A., S. Uzel, S. Vesentini, A. Redaelli, M.J. Buehler, Molecular and mesoscale disease mechanisms of Osteogenesis Imperfecta. Biophysical Journal, 2009. 97(3): 857–865.

    Google Scholar 

  24. Suresh, S., et al., Connections between single-cell biomechanics and human disease states: gastrointestinal cancer and malaria. Acta Biomaterialia, 2005. 1(1): 15–30.

    Article  CAS  Google Scholar 

  25. Cross, S.E., et al., Nanomechanical analysis of cells from cancer patients. Nature Nanotechnology, 2007. 2: 780–783.

    Article  CAS  Google Scholar 

  26. Smith, B.L., et al., Molecular mechanistic origin of the toughness of natural adhesives, fibres and composites. Nature, 1999. 399(6738): 761–763.

    Article  CAS  Google Scholar 

  27. Prater, C.B., H.J. Butt, and P.K. Hansma, Atomic force microscopy. Nature, 1990. 345(6278): 839–840.

    Article  Google Scholar 

  28. Sun, Y.L., et al., Stretching type II collagen with optical tweezers. Journal of Biomechanics, 2004. 37(11): 1665–1669.

    Article  Google Scholar 

  29. Dao, M., C.T. Lim, and S. Suresh, Mechanics of the human red blood cell deformed by optical tweezers. Journal of the Mechanics and Physics of Solids, 2003. 51(11–12): 2259–2280.

    Article  Google Scholar 

  30. Tai, K., F.J. Ulm, and C. Ortiz, Nanogranular origins of the strength of bone. Nano Letters, 2006. 11: 2520–2525

    Article  CAS  Google Scholar 

  31. Lim, C.T., et al., Experimental techniques for single cell and single molecule biomechanics. Materials Science & Engineering C-Biomimetic and Supramolecular Systems, 2006. 26(8): 1278–1288.

    CAS  Google Scholar 

  32. Goddard, W.A., A perspective of materials modeling in Handbook of Materials Modeling, Edited by S. Yip. 2006, Berlin: Springer.

    Google Scholar 

  33. Csete, M.E. and J.C. Doyle, Reverse engineering of biological complexity. Science, 2002. 295(5560): 1664.

    Article  CAS  Google Scholar 

  34. Stelling, J., et al., Robustness of cellular functions. Cell, 2004. 118(6): 675–685.

    Article  CAS  Google Scholar 

  35. Aizenberg, J., et al., Skeleton of Euplectella sp.: Structural hierarchy from the nanoscale to the macroscale. American Association for the Advancement of Science, 2005. 309: 275–278.

    CAS  Google Scholar 

  36. Currey, J.D., Materials science: Hierarchies in biomineral structures. Science, 2005. 309: 253–254.

    Article  CAS  Google Scholar 

  37. Woesz, A., et al., Micromechanical properties of biological silica in skeletons of deep-sea sponges. Journal of Materials Research, 2006. 21(8): 2069.

    Article  Google Scholar 

  38. Horn, J., N. Nafpliotis, and D.E. Goldberg, A niched Pareto genetic algorithm for multiobjective optimization. Evolutionary Computation, 1994. IEEE World Congress on Computational Intelligence, Proceedings of the First IEEE Conference on 1994, pp. 82–87.

    Google Scholar 

  39. Ackbarow, T., et al., Hierarchies, multiple energy barriers and robustness govern the fracture mechanics of alpha-helical and beta-sheet protein domains. Proceedings of the National Academy of Sciences of the United States of America, 2007. 104: 16410–16415

    Article  CAS  Google Scholar 

  40. Ackbarow, T. and M.J. Buehler, Hierarchical coexistence of universality and diversity controls robustness and multi-functionality in protein materials. Theoretical and Computational Nanoscience, 2008. 5(7): 1193–1204.

    Article  CAS  Google Scholar 

  41. Buehler, M.J., S. Keten, and T. Ackbarow, Theoretical and computational hierarchical nanomechanics of protein materials: Deformation and fracture. Progress in Materials Science, 2008. 53(8): 1101–1241.

    Google Scholar 

  42. Tang, Z., et al., Nanostructured artificial nacre. Nature Materials, 2003. 2(6): 413–418.

    Article  CAS  Google Scholar 

  43. Vashishta, P., R.K. Kalia, and A. Nakano, Large-scale atomistic simulations of dynamic fracture. Computing in Science and Engineering, 1999. 1 (5): 56–65.

    Article  CAS  Google Scholar 

  44. Rountree, C.L., et al., Atomistic aspects of crack propagation in brittle materials: Multimillion atom molecular dynamics simulations. Annual Review of Materials Research, 2002. 32: 377–400.

    Article  CAS  Google Scholar 

  45. Buehler, M.J., Atomistic Modeling of Materials Failure. 2008, New York: Springer.

    Book  Google Scholar 

  46. Buehler, M.J. and H.J. Gao, Dynamical fracture instabilities due to local hyperelasticity at crack tips. Nature, 2006. 439(7074): 307–310.

    Article  CAS  Google Scholar 

  47. Buehler, M.J., F.F. Abraham, and H. Gao, Hyperelasticity governs dynamic fracture at a critical length scale. Nature, 2003. 426: 141–146.

    Article  CAS  Google Scholar 

  48. Buehler, M.J. and H. Gao, Ultra large scale atomistic simulations of dynamic fracture in Handbook of Theoretical and Computational Nanotechnology, Edited by W. Schommers and A. Rieth. 2006, Stevenson Ranch, CA: American Scientific Publishers (ASP).

    Google Scholar 

  49. Buehler, M.J., A.C.T.v. Duin, and W.A. Goddard, Multi-paradigm modeling of dynamical crack propagation in silicon using the ReaxFF reactive force field. Physical Review Letters, 2006. 96(9): 095505.

    Article  CAS  Google Scholar 

  50. Buehler, M.J., et al., Threshold crack speed controls dynamical fracture of silicon single crystals. Physical Review Letters, 2007. 99: 165502

    Article  CAS  Google Scholar 

  51. Wang, W., et al., Biomolecular simulations: Recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions. Annual Review of Biophysics and Biomolecular Structure, 2001. 30: 211–243.

    Article  CAS  Google Scholar 

  52. Mackerell, A.D., Empirical force fields for biological macromolecules: Overview and issues. Journal of Computational Chemistry, 2004. 25(13): 1584–1604.

    Article  CAS  Google Scholar 

  53. Deniz, A.A., S. Mukhopadhyay, and E.A. Lemke, Single-molecule biophysics: at the interface of biology, physics and chemistry. Journal of the Royal Society Interface, 2008. 5(18): 15–45.

    Article  CAS  Google Scholar 

  54. Scheraga, H.A., M. Khalili, and A. Liwo, Protein-folding dynamics: Overview of molecular simulation techniques. Annual Review of Physical Chemistry, 2007. 58: 57–83.

    Article  CAS  Google Scholar 

  55. Van der Spoel, D., et al., GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 2005. 26(16): 1701–1718.

    Article  CAS  Google Scholar 

  56. Nelson, M.T., et al., NAMD: A parallel, object oriented molecular dynamics program. International Journal of Supercomputer Applications and High Performance Computing, 1996. 10(4): 251–268.

    Article  Google Scholar 

  57. Ponder, J. and D. Case, Force fields for protein simulations. Protein Simulations, 2003. 66: 27–85.

    Article  CAS  Google Scholar 

  58. MacKerell, A.D., et al., All-atom empirical potential for molecular modeling and dynamics studies of proteins. Journal of Physical Chemistry B, 1998. 102(18): 3586–3616.

    Article  CAS  Google Scholar 

  59. Mayo, S.L., B.D. Olafson, and W.A. Goddard, Dreiding – A generic force-field for molecular simulations. Journal of Physical Chemistry, 1990. 94(26): 8897–8909.

    Article  CAS  Google Scholar 

  60. Rappe, A.K., et al., Uff, a full periodic-table force-field for molecular mechanics and molecular-dynamics simulations. Journal of the American Chemical Society, 1992. 114(25): 10024–10035.

    Article  CAS  Google Scholar 

  61. Pearlman, D.A., et al., Amber, a package of computer-programs for applying molecular mechanics, normal-mode analysis, molecular-dynamics and free-energy calculations to simulate the structural and energetic properties of molecules. Computer Physics Communications, 1995. 91(1–3): 1–41.

    Article  CAS  Google Scholar 

  62. Gao, H., A theory of local limiting speed in dynamic fracture. Journal of the Mechanics and Physics of Solids, 1996. 44(9): 1453–1474.

    Article  CAS  Google Scholar 

  63. Duin, A.C.T.v., et al., ReaxFF: A reactive force field for hydrocarbons. Journal of Physical Chemistry A, 2001. 105: 9396–9409.

    Article  CAS  Google Scholar 

  64. Brenner, D.W., et al., A second-generation reactive empirical bond order (REBO) potential energy expression for hydrocarbons. Journal of Physics-Condensed Matter, 2002. 14(4): 783–802.

    Article  CAS  Google Scholar 

  65. Stuart, S.J., A.B. Tutein, and J.A. Harrison, A reactive potential for hydrocarbons with intermolecular interactions. Journal of Chemical Physics, 2000. 112(14): 6472–6486.

    Article  CAS  Google Scholar 

  66. Strachan, A., et al., Shock waves in high-energy materials: The initial chemical events in nitramine RDX. Physical Review Letters, 2003. 91(9): 098301-1–098301-4.

    Article  CAS  Google Scholar 

  67. Nielson, K.D., et al., Development of the ReaxFF reactive force field for describing transition metal catalyzed reactions, with application to the initial stages of the catalytic formation of carbon nanotubes. Journal of Physical Chemistry A, 2005. 109: 49.

    Article  CAS  Google Scholar 

  68. Duin, A.C.T.v., et al., ReaxFF SiO: Reactive force field for silicon and silicon oxide systems. Journal of Physical Chemistry A, 2003. 107: 3803–3811.

    Article  CAS  Google Scholar 

  69. Han, S.S., et al., Optimization and application of lithium parameters for the reactive force field, ReaxFF. Journal of Physical Chemistry A, 2005. 109(20): 4575–4582.

    Article  CAS  Google Scholar 

  70. Chenoweth, K., et al., Simulations on the thermal decomposition of a poly(dimethylsiloxane) polymer using the ReaxFF reactive force field. Journal of the American Chemical Society, 2005. 127(19): 7192–7202.

    Article  CAS  Google Scholar 

  71. Strachan, A., et al., Thermal decomposition of RDX from reactive molecular dynamics. Journal of Chemical Physics, 2005. 122(5): 054502

    Article  CAS  Google Scholar 

  72. Cheung, S., et al., ReaxFF(MgH) reactive force field for magnesium hydride systems. Journal of Physical Chemistry A, 2005. 109(5): 851–859.

    Article  CAS  Google Scholar 

  73. Chenoweth, K., et al., Development and application of a ReaxFF reactive force field for oxidative dehydrogenation on vanadium oxide catalysts. Journal of Physical Chemistry C, 2005. 112: 14645–14654.

    Google Scholar 

  74. Buehler, M.J., Hierarchical chemo-nanomechanics of stretching protein molecules: Entropic elasticity, protein unfolding and molecular fracture. Journal of Mechanics of Materials and Structures, 2007. 2(6): 1019–1057.

    Article  Google Scholar 

  75. Datta, D., A.C.T.v. Duin, and W.A. Goddard, Extending ReaxFF to Biomacromolecules. Unpublished, 2005.

    Google Scholar 

  76. Buehler, M.J., et al., The Computational Materials Design Facility (CMDF): A powerful framework for multiparadigm multi-scale simulations. Materials Research Society Proceedings, 2006. 894: LL3.8.

    Google Scholar 

  77. Tozzini, V., Coarse-grained models for proteins. Current Opinion in Structural Biology, 2005. 15(2): 144–150.

    Article  CAS  Google Scholar 

  78. Tirion, M., Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Physical Review Letters, 1996. 77(9): 1905–1908.

    Article  CAS  Google Scholar 

  79. Haliloglu, T., I. Bahar, and B. Erman, Gaussian dynamics of folded proteins. Physical Review Letters, 1997. 79(16): 3090–3093.

    Article  CAS  Google Scholar 

  80. Hayward, S. and N. Go, Collective variable description of native protein dynamics. Annual Review of Physical Chemistry, 1995. 46: 223–250.

    Article  CAS  Google Scholar 

  81. West, D.K., et al., Mechanical resistance of proteins explained using simple molecular models. Biophysical Journal, 2006. 90(1): 287–297.

    Article  CAS  Google Scholar 

  82. Dietz, H. and M. Rief, Elastic bond network model for protein unfolding mechanics. Physical Review Letters, 2008. 1(9): 098101-1–098101-4.

    Google Scholar 

  83. Sulkowska, J.I. and M. Cieplak, Mechanical stretching of proteins – a theoretical survey of the Protein Data Bank. Journal of Physics-Condensed Matter, 2007. 19(28): 283201.

    Article  CAS  Google Scholar 

  84. Bathe, M., A finite element framework for computation of protein normal modes and mechanical response. Proteins-Structure Function and Bioinformatics, 2008. 70(4): 1595–1609.

    Article  CAS  Google Scholar 

  85. Bahar, I. and R. Jernigan, Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation. Journal of Molecular Biology, 1997. 266(1): 195–214.

    Article  CAS  Google Scholar 

  86. Nguyen, H. and C. Hall, Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides. Proceedings of the National Academy of Sciences of the United States of America, 2004. 101(46): 16180–16185.

    Article  CAS  Google Scholar 

  87. Nguyen, H. and C. Hall, Spontaneous fibril formation by polyalanines: Discontinuous molecular dynamics simulations. Journal of the American Chemical Society, 2006. 128(6): 1890–1901.

    Article  CAS  Google Scholar 

  88. Arkhipov, A., P. L. Freddolino, et al., Coarse-grained molecular dynamics simulations of a rotating bacterial flagellum. Biophysical Journal, 2006. 91(12): 4589–4597.

    Google Scholar 

  89. Buehler, M.J., Nature designs tough collagen: Explaining the nanostructure of collagen fibrils. Proceedings of the National Academy of Sciences of the United States of America, 2006. 103(33): 12285–12290.

    Article  CAS  Google Scholar 

  90. Buehler, M., Molecular nanomechanics of nascent bone: fibrillar toughening by mineralization. Nanotechnology, 2007. 18(29): 295102.

    Article  CAS  Google Scholar 

  91. Chen, J., W. Im, and C. Brooks, Balancing solvation and intramolecular interactions: Toward a consistent generalized born force field. Journal of the American Chemical Society, 2006. 128(11): 3728–3736.

    Article  CAS  Google Scholar 

  92. Chen, J., C. Brooks, and J. Khandogin, Recent advances in implicit solvent-based methods for biomolecular simulations. Current Opinion in Structural Biology, 2008. 18(2): 140–148.

    CAS  Google Scholar 

  93. Roux, B. and T. Simonson, Implicit solvent models. Biophysical Chemistry, 1999. 78(1–2): 1–20.

    Article  CAS  Google Scholar 

  94. Bertaud, J., Z. Qin, M.J. Buehler, Atomistically informed mesoscale model of alpha-helical protein domains, I International Journal for Multiscale Computational Engineering, 2009. 7(3): 237–250.

    Google Scholar 

  95. Ackbarow, T., D. Sen, C. Thaulow, and M.J. Buehler, Alpha-helical protein networks are self protective and flaw tolerant, PLoS ONE, 2009. 4(6): e6015.

    Google Scholar 

  96. Aebi, U., et al., The nuclear lamina is a meshwork of intermediate-type filaments. Nature, 1986. 323(6088): 560–564.

    Article  CAS  Google Scholar 

  97. Ackbarow, T. and M.J. Buehler, Superelasticity, energy dissipation and strain hardening of vimentin coiled-coil intermediate filaments: Atomistic and continuum studies. Journal of Materials Science, 2007 42(21): 8771–8787.

    Article  CAS  Google Scholar 

  98. Buehler, M.J. and S. Keten, Elasticity, strength and resilience: A comparative study on mechanical signatures of α-helix, β-sheet and tropocollagen domains. Nano Research, 2008. 1(1): 63–71.

    Article  CAS  Google Scholar 

  99. Fudge, D.S., et al., The mechanical properties of hydrated intermediate filaments: Insights from hagfish slime threads. Biophysical Journal, 2003. 85(3): 2015–2027.

    Article  CAS  Google Scholar 

  100. Fudge, D.S. and J.M. Gosline, Molecular design of the alpha-keratin composite: insights from a matrix-free model, hagfish slime threads. Proceedings of the Royal Society of London Series B-Biological Sciences, 2004. 271(1536): 291–299.

    Article  CAS  Google Scholar 

  101. Bell, G.I., Models for the specific adhesion of cells to cells. Science, 1978. 200(4342): 618–627.

    Article  CAS  Google Scholar 

  102. Hanggi, P., P. Talkner, and M. Borkovec, Reaction-rate theory: Fifty years after Kramers. Review of Modern Physics, 1990. 62(2): 251–341.

    Article  Google Scholar 

  103. Zhurkov, S.N., Kinetic concept of the strength of solids. International Journal of Fracture Mechanics, 1965. 1: 311–323.

    CAS  Google Scholar 

  104. Evans, E. and K. Ritchie, Dynamic strength of molecular adhesion bonds. Biophysical Journal, 1997. 72(4): 1541–1555.

    Article  CAS  Google Scholar 

  105. Hyeon, C. and D. Thirumalai, Measuring the energy landscape roughness and the transition state location of biomolecules using single molecule mechanical unfolding experiments. Journal of Physics, Condensed Matter, 2007. 19(11): 113101.

    Article  CAS  Google Scholar 

  106. Seifert, U., Rupture of multiple parallel molecular bonds under dynamic loading. Physical Review Letters, 2000. 84(12): 2750–2753.

    Article  CAS  Google Scholar 

  107. Seifert, U., Dynamic strength of adhesion molecules: Role of rebinding and self-consistent rates. Europhysics Letters, 2002. 58(5): 792–798.

    Article  CAS  Google Scholar 

  108. Evans, E., Probing the relation between force-lifetime-and chemistry in single molecular bonds. Annual Reviews in Biophysics and Biomolecular Structure, 2001. 30(1): 105–128.

    Article  CAS  Google Scholar 

  109. Hummer, G. and A. Szabo, Kinetics from nonequilibrium single-molecule pulling experiments. Biophysical Journal, 2003. 85(1): 5–15.

    Article  CAS  Google Scholar 

  110. Walton, E.B., S. Lee, and K.J. Van Vliet, Extending Bell’s model: How force transducer stiffness alters measured unbinding forces and kinetics of molecular complexes. Biophysical Journal, 2008. 94(7): 2621.

    Article  CAS  Google Scholar 

  111. Zwanzig, R., Diffusion in a rough potential. Proceedings of the National Academy of Sciences of the United States of America, 1988. 85(7): 2029–2030.

    Article  CAS  Google Scholar 

  112. Erdmann, T. and U.S. Schwarz, Stability of adhesion clusters under constant force. Physical Review Letters, 2004. 92(10): 108102.

    Article  CAS  Google Scholar 

  113. Erdmann, T. and U.S. Schwarz, Bistability of cell-matrix adhesions resulting from nonlinear receptor-ligand dynamics. Biophysical Journal, 2006. 91(6): L60.

    Article  CAS  Google Scholar 

  114. Erdmann, T. and U.S. Schwarz, Stability of adhesion clusters under constant force. Physical Review Letters, 2004. 92(10): 4.

    Article  CAS  Google Scholar 

  115. Rief, M., J.M. Fernandez, and H.E. Gaub, Elastically coupled two-level systems as a model for biopolymer extensibility. Physical Review Letters, 1998. 81(21): 4764–4767.

    Article  CAS  Google Scholar 

  116. Dietz, H. and M. Rief, Elastic bond network model for protein unfolding mechanics. Physical Review Letters, 2008. 100(9): 98101.

    Article  CAS  Google Scholar 

  117. Buehler, M.J. and T. Ackbarow, Fracture mechanics of protein materials. Materials Today, 2007. 10(9): 46–58.

    Article  CAS  Google Scholar 

  118. Keten, S. and M.J. Buehler, Asymptotic strength limit of hydrogen bond assemblies in proteins at vanishing pulling rates. Physical Review Letters, 2008. 100: 198301.

    Google Scholar 

  119. Keten, S. and M.J. Buehler, Geometric confinement governs the rupture strength of H-bond assemblies at a critical length scale. Nano Letters, 2008. 8(2): 743–748.

    Article  CAS  Google Scholar 

  120. Yip, S., The strongest size. Nature, 1998. 391: 532–533.

    Article  CAS  Google Scholar 

  121. Wolf, D., et al., Deformation mechanism and inverse Hall-Petch behavior in nanocrystalline materials. Zeitschrift für Metallkunde, 2003. 94: 1052–1061.

    Google Scholar 

  122. Gruber, M. and A.N. Lupas, Historical review: Another 50th anniversary – new periodicities in coiled coils. Trends in Biochemical Sciences, 2003. 28(12): 679–685.

    Article  CAS  Google Scholar 

  123. Moir, R.D. and T.P. Spann, The structure and function of nuclear lamins: implications for disease. Cellular and Molecular Life Sciences, 2001. 58(12–13): 1748–1757.

    Article  CAS  Google Scholar 

  124. Wilson, K.L., M.S. Zastrow, and K.K. Lee, Lamins and disease: Insights into nuclear infrastructure. Cell, 2001. 104(5): 647–650.

    CAS  Google Scholar 

  125. Bryson, J.W., et al., Protein design – a hierarachical approach. Science, 1995. 270(5238): 935–941.

    Article  CAS  Google Scholar 

  126. Kirshenbaum, K., R.N. Zuckermann, and K.A. Dill, Designing polymers that mimic biomolecules. Current Opinion in Structural Biology, 1999. 9(4): 530–535.

    Article  CAS  Google Scholar 

  127. Kim, S. and P.A. Coulombe, Intermediate filament scaffolds fulfill mechanical, organizational, and signaling functions in the cytoplasm. Genes & Development, 2007. 21(13): 1581–1597.

    Article  CAS  Google Scholar 

  128. Herrmann, H., et al., Intermediate filaments: from cell architecture to nanomechanics. Nature Reviews Molecular Cell Biology, 2007. 8(7): 562–573.

    Article  CAS  Google Scholar 

  129. Ackbarow, T., S. Keten, and M.J. Buehler, A multi-timescale strength model of alpha-helical protein domains, Journal of Physics: Condensed Matter, 2009. 21: 035111.

    Google Scholar 

  130. Bell, G.I., Models for specific adhesion of cells to cells. Science, 1978. 200(4342): 618–627.

    Article  CAS  Google Scholar 

  131. Evans, E.A. and D.A. Calderwood, Forces and bond dynamics in cell adhesion. Science, 2007. 316(5828): 1148–1153.

    Article  CAS  Google Scholar 

  132. Evans, E., Probing the relation between force – lifetime – and chemistry in single molecular bonds. Annual Review of Biophysics and Biomolecular Structure, 2001. 30: 105–128.

    Article  CAS  Google Scholar 

  133. Evans, E.B., Looking inside molecular bonds at biological interfaces with dynamic force spectroscopy. Biophysical Chemistry, 1999. 82(2–3): 83–97.

    Article  CAS  Google Scholar 

  134. Merkel, R., et al., Energy landscapes of receptor-ligand bonds explored with dynamic force spectroscopy. Nature (London), 1999. 379(6714): 50–53.

    Google Scholar 

  135. Dudko, O.K., G. Hummer, and A. Szabo, Intrinsic rates and activation free energies from single-molecule pulling experiments. Physical Review Letters, 2006. 96(10): 108101.

    Article  CAS  Google Scholar 

  136. Makarov, D.E., Unraveling individual molecules by mechanical forces: Theory meets experiment. Biophysical Journal, 2007. 92(12): 4135–4136.

    Article  CAS  Google Scholar 

  137. West, D.K., P.D. Olmsted, and E. Paci, Mechanical unfolding revisited through a simple but realistic model. Journal of Chemical Physics, 2006. 124(15): 154909.

    Google Scholar 

  138. Erdmann, T. and U.S. Schwarz, Stability of adhesion clusters under constant force. Physical Review Letters, 2004. 92(10): 108102.

    Article  CAS  Google Scholar 

  139. Lantz, M.A., et al., Stretching the alpha-helix: A direct measure of the hydrogen-bond energy of a single-peptide molecule. Chemical Physics Letters, 1999. 315(1–2): 61–68.

    Article  CAS  Google Scholar 

  140. Kageshima, M., et al., Insight into conformational changes of a single alpha-helix peptide molecule through stiffness measurements. Chemical Physics Letters, 2001. 343(1–2): 77–82.

    Article  CAS  Google Scholar 

  141. Dudko, O.K., et al., Extracting kinetics from single-molecule force spectroscopy: Nanopore unzipping of DNA hairpins. Biophysical Journal, 2007. 92(12): 4188–4195.

    Article  CAS  Google Scholar 

  142. Keten, S. and M.J. Buehler. Strength limit of entropic elasticity in beta-sheet protein domains. Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), 2008. 78(6): 061913.

    Google Scholar 

  143. Griffith, A.A., The phenomenon of rupture and flows in solids. Philosophical Transactions of the Royal Society of London A, 1920. 221: 163–198.

    Google Scholar 

  144. Sheu, S.-Y., et al., Energetics of hydrogen bonds in peptides. PNAS, 2003. 100(22): 12683–12687.

    Article  CAS  Google Scholar 

  145. Rief, M., et al., Single molecule force spectroscopy of spectrin repeats: Low unfolding forces in helix bundles. Journal of Molecular Biology, 1999. 286(2): 553–561.

    Article  CAS  Google Scholar 

  146. Law, R., et al., Influence of lateral association on forced unfolding of antiparallel spectrin heterodimers. Journal of Biological Chemistry, 2004. 279(16): 16410–16416.

    Article  CAS  Google Scholar 

  147. Lenne, P.F., et al., Stales and transitions during forced unfolding of a single spectrin repeat. FEBS Letters, 2000. 476(3): 124–128.

    Article  CAS  Google Scholar 

  148. Law, R., et al., Cooperativity in forced unfolding of tandem spectrin repeats. Biophysical Journal, 2003. 84(1): 533–544.

    Article  CAS  Google Scholar 

  149. Law, R., et al., Pathway shifts and thermal softening in temperature-coupled forced unfolding of spectrin domains. Biophysical Journal, 2003. 85(5): 3286–3293.

    Article  CAS  Google Scholar 

  150. Bernstein, F.C., et al., Protein data bank – computer-based archival file for macromolecular structures. Journal of Molecular Biology, 1977. 112(3): 535–542.

    Article  CAS  Google Scholar 

  151. Kolano, C., et al., Watching hydrogen-bond dynamics in a beta-turn by transient two-dimensional infrared spectroscopy. Nature, 2006. 444(7118): 469–472.

    Article  CAS  Google Scholar 

  152. Grandbois, M., et al., How strong is a covalent bond? Science, 1999. 283(5408): 1727–1730.

    Article  CAS  Google Scholar 

  153. Bustamante, C., et al., Entropic elasticity of lambda-phage DNA. Science, 1994. 265(5178): 1599–1600.

    Article  CAS  Google Scholar 

  154. Marko, J.F. and E.D. Siggia, Stretching DNA. Macromolecules, 1995. 28(26): 8759–8770.

    Article  CAS  Google Scholar 

  155. Zhuang, X., Molecular biology: Unraveling DNA condensation with optical tweezers. Science, 2004. 305(5681): 188–190.

    Article  CAS  Google Scholar 

  156. Lang, M., Lighting up the mechanome, in Frontiers of Engineering: Reports on Leading-Edge Engineering from the 2007 Symposium. 2008, National Academy of Engineering of the National Academies.

    Google Scholar 

  157. Ebenstein, D.M. and L.A. Pruitt, Nanoindentation of biological materials. Nano Today, 2006. 1(3): 26–33.

    Article  Google Scholar 

  158. Bozec, L., et al., Atomic force microscopy of collagen structure in bone and dentine revealed by osteoclastic resorption. Ultramicroscopy, 2005. 105(1–4): 79–89.

    Article  CAS  Google Scholar 

  159. Guzman, C., et al., Exploring the mechanical properties of single vimentin intermediate filaments by atomic force microscopy. Journal of Molecular Biology, 2006. 360(3): 623–630.

    Article  CAS  Google Scholar 

  160. Yuan, C.B., et al., Energy landscape of streptavidin-biotin complexes measured by atomic force microscopy. Biochemistry, 2000. 39(33): 10219–10223.

    Article  CAS  Google Scholar 

  161. Sun, Y.L., Z.P. Luo, and K.N. An, Stretching short biopolymers using optical tweezers. Biochemical and Biophysical Research Communications, 2001. 286(4): 826–830.

    Article  CAS  Google Scholar 

  162. Sazonova, V., et al., A tunable carbon nanotube electromechanical oscillator. Nature, 2004. 431(7006): 284–287.

    Article  CAS  Google Scholar 

  163. Thorsen, T., S.J. Maerkl, and S.R. Quake, Microfluidic large-scale integration. Science, 2002. 298(5593): 580–584.

    Article  CAS  Google Scholar 

  164. Whitesides, G.M. and B. Grzybowski, Self-assembly at all scales. Science, 2002. 295(5564): 2418–2421.

    Article  CAS  Google Scholar 

  165. Yan, H., et al., DNA-templated self-assembly of protein arrays and highly conductive nanowires. Science, 2003. 301(5641): 1882–1884.

    Article  CAS  Google Scholar 

  166. Rho, J.Y., L. Kuhn-Spearing, and P. Zioupos, Mechanical properties and the hierarchical structure of bone. Medical Engineering and Physics, 1998. 20(2): 92–102.

    Article  CAS  Google Scholar 

  167. Currey, J.D., Mechanical properties of mother of pearl in tension. Proceedings of the Royal Society of London. Series B, Biological Sciences, 1977. 196(1125): 443–463.

    Article  Google Scholar 

  168. Menig, R., et al., Quasi-static and dynamic mechanical response of Strombus gigas (conch) shells. Materials Science & Engineering A, 2001. 297(1–2): 203–211.

    Article  Google Scholar 

  169. Tesch, W., et al., Graded microstructure and mechanical properties of human crown dentin. Calcified Tissue International, 2001. 69(3): 147–157.

    Article  CAS  Google Scholar 

  170. Ritchie, R., M.J. Buehler, P. Hansma. The strength and toughness of bone, Physics Today, 2009. 62(6): 41-47.

    Google Scholar 

  171. Taylor, D., J.G. Hazenberg, and T.C. Lee, Living with cracks: Damage and repair in human bone. Nature Materials, 2007. 6(4): 263–266.

    Article  CAS  Google Scholar 

  172. Nalla, R.K., J.J. Kruzic, and R.O. Ritchie, On the origin of the toughness of mineralized tissue: Microcracking or crack bridging? Bone, 2004. 34(5): 790–798.

    Article  CAS  Google Scholar 

  173. Gao, H., et al., From the cover: Materials become insensitive to flaws at nanoscale: Lessons from nature. Proceedings of the National Academy of Sciences of the United States of America, 2003. 100(10): 5597.

    Article  CAS  Google Scholar 

  174. Mann, S., et al., Crystallization at Inorganic-organic Interfaces: Biominerals and biomimetic synthesis. Science, 1993. 261(5126): 1286–1292.

    Article  CAS  Google Scholar 

  175. Gilbert, P., M. Abrecht, and B.H. Frazer, The organic-mineral interface in biominerals. Reviews in Mineralogy and Geochemistry, 2005. 59(1): 157–185.

    Article  CAS  Google Scholar 

  176. Smith, B.L., et al., Molecular mechanistic origin of the toughness of natural adhesives, fibres and composites. Nature, 1999. 399(6738): 761–763.

    Article  CAS  Google Scholar 

  177. Broedling, N.C., et al., The strength limit in a bio-inspired metallic nanocomposite. Journal of Mechanics and Physics of Solids, 2008. 56(3): 1086–1104.

    Article  CAS  Google Scholar 

  178. Sen, D. and M.J. Buehler, Crystal size controlled deformation mechanism: Breakdown of dislocation mediated plasticity in single nanocrystals under geometric confinement. Physical Review B, 2008. 77(19): 195439.

    Article  CAS  Google Scholar 

  179. Sen, D. and M.J. Buehler, Shock loading of bone-inspired metallic nanocomposites. Solid State Phenomena, 2008. 139: 11–22.

    Google Scholar 

  180. Whitesides, G.M., J.P. Mathias, and C.T. Seto, Molecular self-assembly and nanochemistry: A chemical strategy for the synthesis of nanostructures. Science, 1991. 254(5036): 1312–1319.

    Article  CAS  Google Scholar 

  181. Whitesides, G.M. and B. Grzybowski, Self-assembly at all scales. Science, 2002. 295: 2418–2421.

    Article  CAS  Google Scholar 

  182. Bejan, A., Constructal theory: From thermodynamic and geometric optimization to predicting shape in nature. Energy Conversion and Management, 1998. 39(16–18): 1705–1718.

    Article  Google Scholar 

  183. Kim, P., et al., Thermal Transport Measurements of Individual Multiwalled Nanotubes. Physical Review Letters, 2001. 87(21): 215502.

    Article  CAS  Google Scholar 

  184. Balandin, A.A., et al., Superior thermal conductivity of single-layer graphene. Nano Letters, 2008. 8(3): 902–907.

    Article  CAS  Google Scholar 

  185. Meng, G., et al., Controlled fabrication of hierarchically branched nanopores, nanotubes, and nanowires. Proceedings of the National Academy of Sciences of the United States of America, 2005. 102(20): 7074–7078.

    Article  CAS  Google Scholar 

  186. Shinde, S.L. and J.S. Goela, eds. High Thermal Conductivity Materials. 2004, New York: Springer, p. 271.

    Google Scholar 

  187. Langer, R. and D.A. Tirrell, Designing materials for biology and medicine. Nature, 2004. 428(6982): 487–492.

    Article  CAS  Google Scholar 

  188. Zhao, X.J. and S.G. Zhang, Designer self-assembling peptide materials. Macromolecular Bioscience, 2007. 7(1): 13–22.

    Article  CAS  Google Scholar 

  189. Holland, J.H., Hidden Order – How Adaptation Builds Complexity. 1995, Reading, MA: Helix Books.

    Google Scholar 

  190. Ackbarow, T. and M.J. Buehler, Hierarchical coexistence of universality and diversity controls robustness and multi-functionality in protein materials. Journal of Computational and Theoretical Nanoscience, 2008. 5(7): 1193–1204.

    Google Scholar 

  191. Cui, X.Q., et al., Biocatalytic generation of ppy-enzyme-CNT nanocomposite: From network assembly to film growth. Journal of Physical Chemistry C, 2007. 111(5): 2025–2031.

    Article  CAS  Google Scholar 

  192. Hule, R., D. Pochan, Polymer nanocomposites for biomedical application. MRS Bulletin, 2007. 32(4): 5.

    Google Scholar 

  193. Winey, K.I., Vaia R.A., Polymer nanocomposites. MRS Bulletin, 2007. 32(4): 5.

    Google Scholar 

  194. Petka, W.A., et al., Reversible hydrogels from self-assembling artificial proteins. Science, 1998. 281(5375): 389–392.

    Article  CAS  Google Scholar 

  195. Smeenk, J.M., et al., Controlled assembly of macromolecular beta-sheet fibrils. Angewandte Chemie-International Edition, 2005. 44(13): 1968–1971.

    Article  CAS  Google Scholar 

  196. Zhao, X.J. and S.G. Zhang, Molecular designer self-assembling peptides. Chemical Society Reviews, 2006. 35(11): 1105–1110.

    Article  CAS  Google Scholar 

  197. Mershin, A., et al., A classic assembly of nanobiomaterials. Nature Biotechnology, 2005. 23(11): 1379–1380.

    Article  CAS  Google Scholar 

  198. Aebi, U., et al., The nuclear lamina is a meshwork of intermediate-type filaments. Nature, 1986. 323(6088): 560–564.

    Article  CAS  Google Scholar 

  199. Buehler, M.J., Hierarchical chemo-nanomechanics of proteins: Entropic elasticity, protein unfolding and molecular fracture. Journal of Mechanics of Materials and Structures, 2007. 2(6): 1019–1057.

    Article  Google Scholar 

  200. Ashby, M.F., et al., The mechanical properties of natural materials. I. Material property charts. Proceedings of the Mathematical and Physical Sciences, 1995. 450(1938): 123–140.

    Article  Google Scholar 

  201. Fratzl, P., et al., Structure and mechanical quality of the collagen–mineral nano-composite in bone. Journal of Materials Chemistry, 2004. 14(14): 2115–2123.

    Article  CAS  Google Scholar 

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Keten, S., Bertaud, J., Sen, D., Xu, Z., Ackbarow, T., Buehler, M.J. (2010). Multiscale Modeling of Biological Protein Materials – Deformation and Failure. In: Dumitrica, T. (eds) Trends in Computational Nanomechanics. Challenges and Advances in Computational Chemistry and Physics, vol 9. Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-9785-0_17

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