From Nano to Macro: Introduction to Atomistic Modeling Techniques

Readings

LEC #	TOPICS	READINGS
1	Introduction to Mechanics of Materials	Hirth, John Price, and Jens Lothe. Theory of Dislocations. Melbourne, FL: Krieger, 1991, pp. 29-57.
2	Introduction to Classical Molecular Dynamics
3	Mechanics of Ductile Materials	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. 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.
4	Dynamic Fracture of Brittle Materials	Gouldstone, Andrew, Krystyn Van Vliet, and Subra Suresh. “Simulation of a Defect Nucleation in a Crystal.” Nature 411 (2001): 656. Suresh, Subra. Fatigue of Materials. Cambridge, UK: Cambridge University Press, 1991, pp. 283-302.
5	The Cauchy-Born Rule	Rice, James R. “Dislocation Nucleation from a Crack Tip: An Analysis Based on the Peierls Concept.” J Mech Phys Solids 40 (1992): 239-271. 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. 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. 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. 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. 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.
6	Mechanics of Biological Materials	Boal, David. Mechanics of the Cell. Cambridge, UK: Cambridge University Press, 2002, chapters 1, 2, 6, and 7. ISBN: 0521796814. Bao, G., and Subra Suresh. “Cell and Molecular Mechanics of Biological Materials.” Nature Materials 2 (2003): 715-725. Buehler, Markus J. “Large-Scale Hierarchical Molecular Modeling of Nanostructured Biological Materials.” Journal of Computational and Theoretical Nanoscience 3 (2006): 603-623.
7	Introduction to The Problem Set	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. 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. Karplus, Martin and J. Andrew McCammon. “Molecular Dynamics Simulations of Biomolecules.” Nature Structural Biology 9 (2002): 646-652.
8	Size Effects in Deformation of Materials	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. 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. Knap, J. and M. Ortiz. “An analysis of the quasicontinuum method.” Journal of the Mechanics and Physics of Solids 49 (2001): 1899-1923. Final Project Part A Heino, P., H. Häkkinen and K. Kaski. “Molecular-dynamics Study of Mechanical Properties of Copper.” Europhys Lett 41 (1998): 273-278. 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. 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. Mishin, Y. “Structural Stability and Lattice Defects in Copper: Ab Initio, Tight-Binding, and Embedded-Atom Calculations.” Phys Rev B 63 (2001): 1-16. Final project Part B 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. Final project Part C NAMD Tutorial by Markus Buehler (PDF)