3.021J | Spring 2012 | Undergraduate
Introduction to Modeling and Simulation

Part I: Particle and Continuum Methods

The following lectures notes and readings from the first half of this course covering particle and continuum methods are the previous year version as taught by Professor Markus Buehler.

Part I: Particle and Continuum Methods
1 Introduction Lecture notes (PDF - 2.4MB)
2 Basic molecular dynamics

Lecture notes (PDF - 4.3MB)

Komanduri, R., N. Chandrasekaran, et al. “Molecular Dynamics (MD) Simulation of Uniaxial Tension of Some Single-Crystal Cubic Metals at Nanolevel.” International Journal of Mechanical Sciences 43, no. 10 (2001): 2237–60.

3 Property calculation I

Lecture notes (PDF)

Alder, J., and T. Wainwright. “Phase Transition for a Hard Sphere System.” Journal of Chemical Physics 27 (1957): 1208–09.

Rahman, A. “Correlations in the Motion of Atoms in Liquid Argon.” Physical Review 136, no. 2A (1964): A405–11.

Gibson, J. B., et al. “Dynamics of Radiation Damage.” Physical Review 120, no. 4 (1960): 1229–53.

4 Property calculation II

Lecture notes (PDF - 1.8MB)

Cleri, F., et al. “Atomic-Scale Mechanism of Crack-Tip Plasticity: Dislocation Nucleation and Crack-Tip Shielding.” Physical Review Letters 79, no. 7 (1997): 1309–12.

5 How to model chemical interactions I

Lecture notes (PDF - 1.9MB)

Daw, M., and M. Baskes. “Embedded-Atom Method: Derivation and Application to Impurities, Surfaces, and Other Defects in Metals.” Physical Review B 29, no. 12 (1984): 6443–53.

Van Duin, A., et al. “ReaxFF: A Reactive Force Field for Hydrocarbons.” Journal of Chemical Physics A 105, no. 41 (2001): 9396–409.

Buehler, M., et al. “The Dynamical Complexity of Work-Hardening: A Large-Scale Molecular Dynamics Simulation.” Acta Mechanica Sinica 21, no. 2 (2005): 103–11.

6 How to model chemical interactions II Lecture notes (PDF - 3.1MB)
7 Application to modeling brittle materials Lecture notes (PDF - 1.4MB)
8 Reactive potentials and applications I Lecture notes (PDF)
9 Reactive potentials and applications II Lecture notes (PDF - 1.3MB)
10 Applications to biophysics and bionanomechanics I Lecture notes (PDF - 2.7MB)
11 Applications to biophysics and bionanomechanics II

Lecture notes (PDF - 2.1MB)

Buehler, M. “Hierarchical Chemo-Nanomechanics of Proteins: Entropic Elasticity, Protein Unfolding and Molecular Fracture.” Journal of Mechanics of Materials and Structures 2, no. 6 (2007): 1019–57.

Ackbarow, T., et al. “Hierarchies, Multiple Energy Barriers, and Robustness Govern the Fracture Mechanics of α-helical and β-sheet Protein Domains.” Proceedings of the National Academy of Sciences 104, no. 42 (2007): 16410–15.

Ackbarow, T., et al. “Alpha-Helical Protein Networks are Self-Protective and Flaw-Tolerant.” PLoS ONE 4, no. 6 (2009).

12 Review session - Preparation Quiz 1 Lecture notes (PDF - 4.4MB)