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From Nano to Macro: Introduction to Atomistic Modeling Techniques

Graduate · Historical course

January IAP 2007

The objective of this course is to introduce large-scale atomistic modeling techniques and highlight its importance for solving problems in modern engineering sciences. We demonstrate how atomistic modeling can be used to understand how materials fail under extreme loading, involving unfolding of proteins and propagation of cracks. This course was featured in an MIT {{% resource_link "02431546-003d-43e9-87d6-5c46b918c6fc" "Tech Talk article." %}}

Readings

  • Hirth, John Price, and Jens Lothe. Theory of Dislocations . Melbourne, FL: Krieger, 1991, pp. 29-57.
    Listed reading
  • Zhou, Min. “A New Look at the Atomic Level Virial Stress: On Continuum-Molecular System Equivalence.” Proc R Soc Lond A 459 (2003): 2347-2392.
    Listed reading
  • Zimmerman, J. A., E. B. Webb III, J. J. Hoyt, R. E. Jones, P. A. Klein, and D. J. Bammann. “Calculation of Stress in Atomistic Simulation.” Modelling Simul Mater Sci Eng 12 (2004): S319-S332.
    Listed reading
  • Gouldstone, Andrew, Krystyn Van Vliet, and Subra Suresh. “Simulation of a Defect Nucleation in a Crystal.” Nature 411 (2001): 656.
    Listed reading
  • Suresh, Subra. Fatigue of Materials . Cambridge, UK: Cambridge University Press, 1991, pp. 283-302.
    Listed reading
  • Rice, James R. “Dislocation Nucleation from a Crack Tip: An Analysis Based on the Peierls Concept.” J Mech Phys Solids 40 (1992): 239-271.
    Listed reading
  • Daw, Murray S., and M. I. Baskes. “Embedded-atom Method: Derivation and Application to Impurities, Surfaces, and Other Defects in Metals.” Phys Rev B 29 (1984): 6443-6453.
    Listed reading
  • Foiles, S. M., M. I. Baskes, and M. S. Daw. “Embedded-Atom-Method Functions for the Fcc Metals Cu, Ag, Nu, Ni, Pd, Pt, and Their Alloys.” Phys Rev B 33 (1986): 7983-7991.
    Listed reading
  • Buehler, Markus J., and Huajian Gao. “Ultra-Large Scale Simulations of Dynamic Materials Failure.” Chapter 14 in Handbook of Theoretical and Computational Nanotechnology . Edited by Michael Rieth and Wolfram Schommers. Stevenson Ranch, CA: American Scientific Publishers, 2005. ISBN: 158883042X.
    Listed reading
  • Buehler, Markus J., Alexander Hartmaier, Mark A. Duchaineau, Farid F. Abraham, Huajian Gao. “The Dynamical Complexity of Work-hardening: A Large-scale Molecular Dynamics Simulation.” Acta Mech Sinica 21 (2005): 103-111.
    Listed reading
  • Buehler, Markus J., Farid F. Abraham, and Huajian Gao. “Stress and Energy Flow Field Near a Rapidly Propagating Mode I Crack.” In Multiscale Modelling and Simulation. Edited by T. Barth et al. Berlin, Germany: Springer Verlag, 2004, pp. 143-156.
    Listed reading
  • Boal, David. Mechanics of the Cell . Cambridge, UK: Cambridge University Press, 2002, chapters 1, 2, 6, and 7. ISBN: 0521796814.
    Listed reading
  • Bao, G., and Subra Suresh. “Cell and Molecular Mechanics of Biological Materials.” Nature Materials 2 (2003): 715-725.
    Listed reading
  • Buehler, Markus J. “Large-Scale Hierarchical Molecular Modeling of Nanostructured Biological Materials.” Journal of Computational and Theoretical Nanoscience 3 (2006): 603-623.
    Listed reading
  • Mayo, Stephen L., Barry D. Olafson and William A. Goddard III. “DREIDING: A Generic Force Field for Molecular Simulations.” J Phys Chem 94 (1990): 8897-8909.
    Listed reading
  • Wang, Wei, Oreola Donini, Carolina M. Reyes, Peter A. Kollman. “Biomolecular Simulations: Recent Developments in Force Fields, Simulations of Enzyme Catalysis, Protein-Ligand, Protein-Protein, and Protein-Nucleic Acid Noncovalent Interactions.” Ann Rev Biophys Biomol Struct 30 (2001): 211-243.
    Listed reading
  • Karplus, Martin and J. Andrew McCammon. “Molecular Dynamics Simulations of Biomolecules.” Nature Structural Biology 9 (2002): 646-652.
    Listed reading
  • Buehler, M. J., H. Yao, B. Ji, and H. Gao. “Cracking and Adhesion at Small Scales: Atomistic and Continuum Studies of Flaw Tolerant Nanostructures.” Modelling and Simulation in Materials Science and Engineering 14 (2006): 799-816.
    Listed reading
  • Miller, Ronald E. and E. B. Tadmor. “The Quasicontinuum Method: Overview, Applications and Current Directions.” Journal of Computer-Aided Materials Design 9 (2002): 203-239.
    Listed reading
  • Knap, J. and M. Ortiz. “An analysis of the quasicontinuum method.” Journal of the Mechanics and Physics of Solids 49 (2001): 1899-1923.
    Listed reading
  • Heino, P., H. Häkkinen and K. Kaski. “Molecular-dynamics Study of Mechanical Properties of Copper.” Europhys Lett 41 (1998): 273-278.
    Listed reading
  • Komanduri, R., N. Chandrasekaran, and L. M. Raff. “Molecular Dynamics (MD) Simulation of Uniaxial Tension of Some Single-Crystal Cubic Metals at Nanolevel.” International Journal of Mechanical Sciences 43 (2001): 2237-2260.
    Listed reading
  • Cleri, Fabrizio, Sidney Yip, Dieter Wolf, and Simon R. Phillpot. “Atomic-Scale Mechanism of Crack-Tip Plasticity: Dislocation Nucleation and Crack-Tip Shielding.” Phys Rev Lett 79 (1997): 1309-1312.
    Listed reading
  • Mishin, Y. “Structural Stability and Lattice Defects in Copper: Ab Initio, Tight-Binding, and Embedded-Atom Calculations.” Phys Rev B 63 (2001): 1-16.
    Listed reading
  • Buehler, Markus J., Jef Dodson, Adri C. T. van Duin, Peter Meulbroek, William A. Goddard III. “The Computational Materials Design Facility (CMDF): A Powerful Framework for Multi-paradigm Multi-scale Simulations.” Mater Res Soc Symp Proc 894 (2006): 0894-LL03-03.1-03.6.
    Listed reading
Sources