From Nano to Macro: Introduction to Atomistic Mode

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From Nano to Macro: Introduction to Atomistic Mode posted by member150_php on 2/28/2009

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From Nano to Macro: Introduction to Atomistic Modeling Techniques

January (IAP) 2007

A model of the mechanical behavior in materials.

Model of the mechanical behavior of materials. (Image by Dr. Markus Buehler.)

Course Highlights

This course features complete sets of lecture notes and assignments. This course is offered during the Independent Activities Period (IAP), which is a special 4-week term at MIT that runs from the first week of January until the end of the month.

Course Description

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 Tech Talk article.

Technical Requirements

Special software is required to use some of the files in this course: .m.

Special software is required to use some of the files in this course: .dcd, .psf, .xyz, and .coor files are the input files.

Syllabus

Class Description

Summary

We introduce atomistic modeling techniques and its importance for solving problems in modern engineering sciences, with an emphasis on mechanical properties. We demonstrate how atomistic modeling can be used to understand how materials fail under extreme loading, involving unfolding of proteins and propagation of cracks. Students will learn the basics of atomistic modeling, including choosing interatomic potentials, visualization and data analysis. We cover basic concepts of mechanics at small scales and relate it to common engineering concepts (e.g. beam theory). Students will also work on hands-on simulation projects.

Goal

After the class, students should have a basic understanding about the fundamentals, application areas and potential of classical molecular dynamics for problems in mechanics of materials. Particular emphasis is on developing a sensitivity for the significance of mechanics in different areas, and how atomistic and continuum viewpoints can be coupled.

Grading Policy

This course is graded P/D/F. There will be several homework assignments that consist of research articles, problem sets and short essays. Due at the end will be a larger computational project for which students will use the GenePattern Web site.

Calendar

Course calendar.
LEC #	TOPICS	KEY DATES
1	Introduction to Mechanics of Materials Basic concepts of mechanics, stress and strain, deformation, strength and fracture
2	Introduction to Classical Molecular Dynamics Introduction into the molecular dynamics simulation; numerical techniques
3	Mechanics of Ductile Materials Dislocations; crystal structures; deformation of metals	Problem set 1 due
4	Dynamic Fracture of Brittle Materials Nonlinear elasticity in dynamic fracture, geometric confinement, interfaces
5	The Cauchy-Born Rule Calculation of elastic properties of atomic lattices
6	Mechanics of Biological Materials Atomistic modeling of fracture of a nanocrystal of copper. All simulation codes and numerical tools will be explained in detail.
7	Introduction to The Problem Set Atomistic modeling of fracture of a nanocrystal of copper. All simulation codes and numerical tools will be explained in detail.	Problem set 2 due
8	Size Effects in Deformation of Materials Size effects in deformation of materials: Is smaller stronger?
		Final project due

Readings

Course 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)