Abstract
Computer simulation has emerged as a powerful tool to investigate and design materials without ever making them. Predicting the properties and behavior of materials by computer simulation from the bottom-up perspective has long been a vision of computational materials scientists and, as computational power increases, modeling and simulation tools are becoming crucial to the investigation of material systems. The key to achieving this goal is using hierarchies of paradigms that seamlessly connect quantum mechanics to macroscopic systems. Particular progress has been made in relating molecular-scale chemistry to mesoscopic and macroscopic material properties essential to define the materiome. This chapter reviews large-scale atomistic and coarse-grain modeling methods commonly implemented to investigate the properties and behavior of natural and biological materials with nanostructured hierarchies. We present basic concepts of hierarchical multiscale modeling capable of providing a bottom-up description of chemically complex materials and some example applications related to the study of collagen material at different hierarchical levels.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
Bibliography
B. J. Alder and T. E. Wainwright. Phase transition for a hard sphere system. Journal of Chemical Physics, 27(5):1208–1209, 1957.
B. J. Alder and T. E. Wainwright. Studies in molecular dynamics .1. general method. Journal of Chemical Physics, 31(2):459–466, 1959.
B. J. Alder and T. E. Wainwright. Studies in molecular dynamics .2. behavior of a small number of elastic spheres. Journal of Chemical Physics, 33(5):1439–1451, 1960.
R. M. Alexander. Elastic energy stores in running vertebrates. American Zoologist, 24(1):85–94, 1984.
R.M. Alexander. Animal Mechanics. Blackwell Scientific, Oxford, UK, 2nd edition edition, 1983.
K. Beck, V. C. Chan, N. Shenoy, A. Kirkpatrick, J. A. M. Ramshaw, and B. Brodsky. Destabilization of osteogenesis imperfecta collagenlike model peptides correlates with the identity of the residue replacing glycine. P. Natl. Acad. Sci. USA, 97(8):4273–4278, 2000.
G. I. Bell. Theoretical-models for the specific adhesion of cells to cells or to surfaces. Advances in Applied Probability, 12(3):566–567, 1980.
J. Bella, M. Eaton, B. Brodsky, and H. M. Berman. Crystal-structure and molecular-structure of a collagen-like peptide at 1.9-angstrom resolution. Science, 266(5182):75–81, 1994.
R. Bhowmik, K. S. Katti, and D. R. Katti. Mechanics of molecular collagen is influenced by hydroxyapatite in natural bone. Journal of Materials Science, 42(21):8795–8803, 2007.
R. Bhowmik, K. S. Katti, and D. R. Katti. Mechanisms of load-deformation behavior of molecular collagen in hydroxyapatite-tropocollagen molecular system: Steered molecular dynamics study. Journal of Engineering Mechanics-Asce, 135(5):413–421, 2009.
B. Brodsky and J. A. M. Ramshaw. The collagen triple-helix structure. Matrix Biology, 15(8-9):545–554, 1997.
M. J. Buehler and S. Keten. Colloquium: Failure of molecules, bones, and the earth itself. Reviews of Modern Physics, 82(2):1459–1487, 2010.
M.J. Buehler. Atomistic and continuum modeling of mechanical properties of collagen: Elasticity, fracture and self-assembly. J. Mater. Res., 21(8): 1947–1961, 2006a.
M.J. Buehler. Nature designs tough collagen: Explaining the nanostructure of collagen fibrils. P. Natl. Acad. Sci. USA, 103(33):1228512290, 2006b.
M.J. Buehler and S.Y. Wong. Entropic elasticity controls nanomechanics of single tropocollagen molecules. Biophysical Journal, 93(1):37–43, 2007.
P. Chamberlain, R. Drewello, L. Korn, W. Bauer, T. Gough, A. Al-Fouzan, M. Collins, N. Van Doorn, O. Craig, and C. Heron. Construction of the khoja zaynuddin mosque: use of animal glue modified with urine. Archaeometry, 53:830–841, 2011.
P. Y. Chou and G. D. Fasman. Prediction of protein conformation. Biochemistry, 13(2):222–245, 1974.
S. W. Cranford and M. J. Buehler. Biomateriomics, volume 165 of Springer Series in Materials Science. Springer Netherlands, 2012.
S. W. Cranford, J. de Boer, C. van Blitterswijk, and M. J. Buehler. Materiomics: An -omics approach to biomaterials research. Adv Mater, 2013.
J.D. Currey. Bones: Structure and Mechanics. Princeton University Press, Princeton, NJ, 2002.
A. A. Deniz, S. Mukhopadhyay, and E. A. Lemke. Single-molecule biophysics: at the interface of biology, physics and chemistry. Journal of the Royal Society Interface, 5(18):15–45, 2008.
S. J. Eppell, B. N. Smith, H. Kahn, and R. Ballarini. Nano measurements with micro-devices: mechanical properties of hydrated collagen fibrils. Journal Of The Royal Society Interface, 3(6):117–121, 2006.
D. R. Eyre, M. A. Weis, and J. J. Wu. Advances in collagen cross-link analysis. Methods, 45:65–74, 2008.
P. Fratzl. Collagen: Structure and Mechanics. Springer, 2008.
P. Fratzl and R. Weinkamer. Nature’s hierarchical materials. Progress in Material Science, 52:1263–1334, 2007.
P. Fratzl, N. Fratzlzelman, and K. Klaushofer. Collagen packing and mineralization - an x-ray-scattering investigation of turkey leg tendon. Biophysical Journal, 64(1):260–266, 1993.
P. Fratzl, K. Misof, I. Zizak, G. Rapp, H. Amenitsch, and S. Bernstorff. Fibrillar structure and mechanical properties of collagen. Journal of Structural Biology, 122(1-2):119–122, 1998.
Y. C. Fung. Elasticity of soft tissues in simple elongation. Am J Physiol, 213(6):1532–44, 1967.
A. Gautieri, S. Vesentini, F. M. Montevecchi, and A. Redaelli. Mechanical properties of physiological and pathological models of collagen peptides investigated via steered molecular dynamics simulations. Journal of Biomechanics, 41(14):3073–3077, 2008.
A. Gautieri, M. J. Buehler, and A. Redaelli. Deformation rate controls elasticity and unfolding pathway of single tropocollagen molecules. Journal of the Mechanical Behavior of Biomedical Materials, 2(2):130–137, 2009.
A. Gautieri, A. Russo, S. Vesentini, A. Redaelli, and M. J. Buehler. Coarsegrained model of collagen molecules using an extended martini force field. Journal of Chemical Theory and Computation, 6(4):1210–1218, 2010.
A. Gautieri, S. Vesentini, A. Redaelli, and M. J. Buehler. Hierarchical structure and nanomechanics of collagen microfibrils from the atomistic scale up. Nano Letters, 11(2):757–766, 2011.
A. Gautieri, S. Vesentini, A. Redaelli, and M. J. Buehler. Viscoelastic properties of model segments of collagen molecules. Matrix Biology, 31 (2):141–149, 2012.
B. R. Gelin and M. Karplus. Sidechain torsional potentials and motion of amino-acids in proteins - bovine pancreatic trypsin-inhibitor. Proceedings of the National Academy of Sciences of the United States of America, 72 (6):2002–2006, 1975.
H. S. Gupta, W. Wagermaier, G. A. Zickler, D. R. B. Aroush, S. S. Funari, P. Roschger, H. D. Wagner, and P. Fratzl. Nanoscale deformation mechanisms in bone. Nano Letters, 5(10):2108–2111, 2005.
R. Harley, D. James, A. Miller, and J. W. White. Phonons and the elastic moduli of collagen and muscle. Nature, 267(5608):285–7, 1977.
R. C. Haut and R. W. Little. A constitutive equation for collagen fibers. J Biomech, 5(5):423–30, 1972.
K. E. Kadler, C. Baldock, J. Bella, and R. P. Boot-Handford. Collagens at a glance. Journal of Cell Science, 120(12):1955–1958, 2007.
M. Levitt and A. Warshel. Computer-simulation of protein folding. Nature, 253(5494):694–698, 1975.
C. A. Lopez, A. J. Rzepiela, A. H. de Vries, L. Dijkhuizen, P. H. Hunenberger, and S. J. Marrink. Martini coarse-grained force field: Extension to carbohydrates. Journal of Chemical Theory and Computation, 5(12): 3195–3210, 2009.
A. C. Lorenzo and E. R. Caffarena. Elastic properties, young’s modulus determination and structural stability of the tropocollagen molecule: a computational study by steered molecular dynamics. Journal Of Biomechanics, 38(7):1527–1533, 2005.
A. D. Mackerell. Empirical force fields for biological macromolecules: Overview and issues. Journal of Computational Chemistry, 25(13):1584–1604, 2004.
A. D. MacKerell, D. Bashford, M. Bellott, R. L. Dunbrack, J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus. All-atom empirical potential for molecular modeling and dynamics studies of proteins. Journal of Physical Chemistry B, 102(18):3586–3616, 1998.
S. J. Marrink, H. J. Risselada, S. Yefimov, D. P. Tieleman, and A. H. de Vries. The martini force field: coarse grained model for biomolecular simulations. Journal of Physical Chemistry B, 111(27):7812–24, 2007.
J. A. Mccammon, B. R. Gelin, and M. Karplus. Dynamics of folded proteins. Nature, 267(5612):585–590, 1977.
N. Metropolis, A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and E. Teller. Equation of state calculations by fast computing machines. Journal of Chemical Physics, 21(6):1087–1092, 1953.
L. Monticelli, S. K. Kandasamy, X. Periole, R. G. Larson, D. P. Tieleman, and S. J. Marrink. The martini coarse-grained force field: Extension to proteins. Journal of Chemical Theory and Computation, 4(5):819–834, 2008.
K. Nakajima and T. Nishi. Nanoscience of single polymer chains revealed by nanofishing. Chemical Record, 6(5):249–258, 2006.
M. T. Nelson, W. Humphrey, A. Gursoy, A. Dalke, L. V. Kale, R. D. Skeel, and K. Schulten. Namd: A parallel, object oriented molecular dynamics program. International Journal Of Supercomputer Applications And High Performance Computing, 10(4):251–268, 1996.
F. H. M. Nestler, S. Hvidt, J. D. Ferry, and A. Veis. Flexibility of collagen determined from dilute-solution viscoelastic measurements. Biopolymers, 22(7):1747–1758, 1983.
J.P.R.O. Orgel, T.C. Irving, A. Miller, and T. J. Wess. Microfibrillar structure of type i collagen in situ. P. Natl. Acad. Sci. USA, 103(24):9001–9005, 2006.
D. A. Pearlman, D. A. Case, J. W. Caldwell, W. S. Ross, T. E. Cheatham, S. Debolt, D. Ferguson, G. Seibel, and P. Kollman. 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, 91(1-3):1–41, 1995.
E. Pena, J. A. Pena, and M. Doblare. On modelling nonlinear viscoelastic effects in ligaments. Journal of Biomechanics, 41(12):2659–2666, 2008.
J. A. Petruska and A. J. Hodge. Subunit model for tropocollagen macromolecule. Proceedings of the National Academy of Sciences of the United States of America, 51(5):871–&, 1964.
S. Plimpton. Fast parallel algorithms for short-range molecular-dynamics. Journal of Computational Physics, 117(1):1–19, 1995.
J. W. Ponder and D. A. Case. Force fields for protein simulations, volume 66 of Advances In Protein Chemistry, pages 27–+. 2003.
R. Puxkandl, I. Zizak, O. Paris, J. Keckes, W. Tesch, S. Bernstorff, P. Purslow, and P. Fratzl. Viscoelastic properties of collagen: synchrotron radiation investigations and structural model. Philosophical Transactions Of The Royal Society Of London Series B-Biological Sciences, 357(1418):191–197, 2002.
Z. Qin and M. J. Buehler. Molecular dynamics simulation of the alphahelix to beta-sheet transition in coiled protein filaments: Evidence for a critical filament length scale. Physical Review Letters, 104(19), 2010.
A. Rahman and Stilling.Fh. Molecular dynamics study of liquid water. Journal of Chemical Physics, 55(7):3336–&, 1971.
Kartha G. Ramachandran, G.N. Structure of collagen. Nature, 176:593595, 1955.
A. K. Rappe, C. J. Casewit, K. S. Colwell, W. A. Goddard, and W. M. Skiff. Uff, a full periodic-table force-field for molecular mechanics and molecular-dynamics simulations. Journal of the American Chemical Society, 114(25):10024–10035, 1992.
F. Rauch and F. H. Glorieux. Osteogenesis imperfecta. The Lancet, 363: 1377–85, 2004.
A. Redaelli, S. Vesentini, M. Soncini, P. Vena, S. Mantero, and F. M. Montevecchi. Possible role of decorin glycosaminoglycans in fibril to fibril force transfer in relative mature tendons - a computational study from molecular to microstructural level. Journal Of Biomechanics, 36(10): 1555–1569, 2003.
A. Rich and F.H.C. Crick. The structure of collagen. Nature, 176:915–916, 1955.
B. J. Rigby, N. Hirai, J. D. Spikes, and H. Eyring. The mechanical properties of rat tail tendon. J Gen Physiol, 43(2):265–83, 1959.
T. Saito, N. Iso, H. Mizuno, N. Onda, H. Yamato, and H. Odashima. Semi-flexibility of collagens in solution. Biopolymers, 21(4):715–728, 1982.
M. S. Sansom, K. A. Scott, and P. J. Bond. Coarse-grained simulation: a high-throughput computational approach to membrane proteins. Biochemical Society Transactions, 36(Pt 1):27–32, 2008.
N. Sasaki and S. Odajima. Elongation mechanism of collagen fibrils and force-strain relations of tendon at each level of structural hierarchy. Journal Of Biomechanics, 29(9):1131–1136, 1996.
N. Sasaki, N. Shukunami, N. Matsushima, and Y. Izumi. Time-resolved x-ray diffraction from tendon collagen during creep using synchrotron radiation. Journal of Biomechanics, 32(3):285–292, 1999.
H. A. Scheraga, M. Khalili, and A. Liwo. Protein-folding dynamics: Overview of molecular simulation techniques. Annual Review of Physical Chemistry, 58:57–83, 2007.
H. R. C. Screen, A. Anssari-Benam, and D. L. Bader. A combined experimental and modelling approach to aortic valve viscoelasticity in tensile deformation. Journal of Materials Science-Materials in Medicine, 22(2): 253–262, 2011.
Z. L. Shen, M. R. Dodge, H. Kahn, R. Ballarini, and S. J. Eppell. Stressstrain experiments on individual collagen fibrils. Biophysical Journal, 95 (8):3956–3963, 2008.
Z. L. Shen, H. Kahn, R. Ballarini, and S. J. Eppell. Viscoelastic properties of isolated collagen fibrils. Biophys J, 100(12):3008–15, 2011.
Z. L. L. Shen, M. R. Dodge, H. Kahn, R. Ballarini, and S. J. Eppell. In vitro fracture testing of submicron diameter collagen fibril specimens. Biophysical Journal, 99(6):1986–1995, 2010.
F. H. Silver, D. L. Christiansen, P. B. Snowhill, and Y. Chen. Transition from viscous to elastic-based dependency of mechanical properties of selfassembled type i collagen fibers. Journal of Applied Polymer Science, 79 (1):134–142, 2001.
M. Srinivasan, S. G. M. Uzel, A. Gautieri, S. Keten, and M. J. Buehler. Alport syndrome mutations in type iv tropocollagen alter molecular structure and nanomechanical properties. Journal of Structural Biology, 168 (3):503–510, 2009.
Y. L. Sun, Z. P. Luo, A. Fertala, and K. N. An. Direct quantification of the flexibility of type i collagen monomer. Biochemical And Biophysical Research Communications, 295(2):382–386, 2002.
R. B. Svensson, T. Hassenkam, P. Hansen, and S. P. Magnusson. Viscoelastic behavior of discrete human collagen fibrils. Journal of the Mechanical Behavior of Biomedical Materials, 3(1):112–115, 2010a.
Ren B. Svensson, Tue Hassenkam, Colin A. Grant, and S. Peter Magnusson. Tensile properties of human collagen fibrils and fascicles are insensitive to environmental salts. Biophysical Journal, 99(12):4020–4027, 2010b.
V. Tozzini. Coarse-grained models for proteins. Current Opinion in Structural Biology, 15(2):144–150, 2005.
H. Utiyama, K. Sakato, K. Ikehara, T. Setsuiye, and M. Kurata. Flexibility of tropocollagen from sedimentation and viscosity. Biopolymers, 12(1): 53–64, 1973.
Joost A. J. van der Rijt, Kees O. van der Werf, Martin L. Bennink, Pieter J. Dijkstra, and Jan Feijen. Micromechanical testing of individual collagen fibrils. Macromolecular Bioscience, 6(9):697–702, 2006.
D. Van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark, and H. J. C. Berendsen. Gromacs: Fast, flexible, and free. Journal of Computational Chemistry, 26(16):1701–1718, 2005.
W. Wang, O. Donini, C. M. Reyes, and P. A. Kollman. 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, 30:211–243, 2001.
X. T. Wang and R. F. Ker. Creep-rupture of wallaby tail tendons. Journal of Experimental Biology, 198(3):831–845, 1995.
S. Weiner and H. D. Wagner. The material bone: Structure mechanical function relations. Annual Review Of Materials Science, 28:271–298, 1998.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 CISM, Udine
About this chapter
Cite this chapter
Gautieri, A., Buehler, M.J. (2013). Multi-scale modeling of biomaterials and tissues. In: Buehler, M.J., Ballarini, R. (eds) Materiomics: Multiscale Mechanics of Biological Materials and Structures. CISM International Centre for Mechanical Sciences, vol 546. Springer, Vienna. https://doi.org/10.1007/978-3-7091-1574-9_2
Download citation
DOI: https://doi.org/10.1007/978-3-7091-1574-9_2
Publisher Name: Springer, Vienna
Print ISBN: 978-3-7091-1573-2
Online ISBN: 978-3-7091-1574-9
eBook Packages: EngineeringEngineering (R0)