 
Abstract/Syllabus:

Buehler, Markus, 1.978 From Nano to Macro: Introduction to Atomistic Modeling Techniques, January IAP 2007. (Massachusetts Institute of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed 08 Jul, 2010). License: Creative Commons BYNCSA
From Nano to Macro: Introduction to Atomistic Modeling Techniques
January (IAP) 2007
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 4week 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 largescale 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 handson 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 CauchyBorn 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 



Further Reading:

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. 2957.

2 
Introduction to Classical Molecular Dynamics


3 
Mechanics of Ductile Materials

Zhou, Min. "A New Look at the Atomic Level Virial Stress: On ContinuumMolecular System Equivalence." Proc R Soc Lond A 459 (2003): 23472392.
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): S319S332.

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. 283302.

5 
The CauchyBorn Rule

Rice, James R. "Dislocation Nucleation from a Crack Tip: An Analysis Based on the Peierls Concept." J Mech Phys Solids 40 (1992): 239271.
Daw, Murray S., and M. I. Baskes. "Embeddedatom Method: Derivation and Application to Impurities, Surfaces, and Other Defects in Metals." Phys Rev B 29 (1984): 64436453.
Foiles, S. M., M. I. Baskes, and M. S. Daw. "EmbeddedAtomMethod Functions for the Fcc Metals Cu, Ag, Nu, Ni, Pd, Pt, and Their Alloys." Phys Rev B 33 (1986): 79837991.
Buehler, Markus J., and Huajian Gao. "UltraLarge 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 Workhardening: A Largescale Molecular Dynamics Simulation." Acta Mech Sinica 21 (2005): 103111.
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. 143156.

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): 715725.
Buehler, Markus J. "LargeScale Hierarchical Molecular Modeling of Nanostructured Biological Materials." Journal of Computational and Theoretical Nanoscience 3 (2006): 603623.

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): 88978909.
Wang, Wei, Oreola Donini, Carolina M. Reyes, Peter A. Kollman. "Biomolecular Simulations: Recent Developments in Force Fields, Simulations of Enzyme Catalysis, ProteinLigand, ProteinProtein, and ProteinNucleic Acid Noncovalent Interactions." Ann Rev Biophys Biomol Struct 30 (2001): 211243.
Karplus, Martin and J. Andrew McCammon. "Molecular Dynamics Simulations of Biomolecules." Nature Structural Biology 9 (2002): 646652.

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): 799816.
Miller, Ronald E. and E. B. Tadmor. "The Quasicontinuum Method: Overview, Applications and Current Directions." Journal of ComputerAided Materials Design 9 (2002): 203239.
Knap, J. and M. Ortiz. "An analysis of the quasicontinuum method." Journal of the Mechanics and Physics of Solids 49 (2001): 18991923.
Final Project Part A
Heino, P., H. Häkkinen and K. Kaski. "Moleculardynamics Study of Mechanical Properties of Copper." Europhys Lett 41 (1998): 273278.
Komanduri, R., N. Chandrasekaran, and L. M. Raff. "Molecular Dynamics (MD) Simulation of Uniaxial Tension of Some SingleCrystal Cubic Metals at Nanolevel." International Journal of Mechanical Sciences 43 (2001): 22372260.
Cleri, Fabrizio, Sidney Yip, Dieter Wolf, and Simon R. Phillpot. "AtomicScale Mechanism of CrackTip Plasticity: Dislocation Nucleation and CrackTip Shielding." Phys Rev Lett 79 (1997): 13091312.
Mishin, Y. "Structural Stability and Lattice Defects in Copper: Ab Initio, TightBinding, and EmbeddedAtom Calculations." Phys Rev B 63 (2001): 116.
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 Multiparadigm Multiscale Simulations." Mater Res Soc Symp Proc 894 (2006): 0894LL0303.103.6.
Final project Part C
NAMD Tutorial by Markus Buehler (PDF)




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