University of Virginia, Department of Materials Science and Engineering

Spring 2016, Tuesday and Thursday, 9:30 - 10:45 am
Wilsdorf Hall 101

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MSE 4270/6270: Introduction to Atomistic Simulations

Instructor: Leonid V. Zhigilei
Office: Wilsdorf Hall, Room 303D
Office Hours: open
Telephone: (434) 243 3582


Class e-mail list: e-mail

Main text: Handouts and lecture notes (Handouts will appear in this page as course progresses).

Books for the course (including books placed on reserve circulate) are listed here.

Grading: Term project 50%, Homework 40%, Presentation/discussion of a published research articles 10%

Homework #1 was due Thursday, February 4
Homework #2 was due Tuesday, February 16
Homework #3 was due Tuesday, February 23
Homework #4 was due Thursday, March 3
Homework #5 was due Thursday, March 17
Homework #6 was due Thursday, March 31
Mini-symposium (presentation of term projects): 9:00 am - 5:00 pm, Sunday, May 8, 2016, Wilsdorf Hall 101
Tentative program of the mini-symposium can be found here


The course introduces students to atomic-level computational methods commonly used in Materials Science, Physics, Chemistry, and Mechanical Engineering. The molecular dynamics and Monte Carlo methods are discussed in depth, from the introduction to the basic concepts to the overview of the current state-of-the-art. Some of the emerging methods for mesoscopic and multiscale modeling are also discussed in the context of real materials-related problems (mechanical and thermodynamic properties, phase transformations, microstructure evolution during processing). Success stories and limitations of contemporary computational methods are considered.

The emphasis of the course is on getting practical experience in designing and performing computer simulations. Pre-written codes implementing atomistic computational methods will be provided. Students will use and modify the pre-written codes and write their own simulation and data analysis codes while working on their homework assignments and term projects. A set of example problems for term project will be provided, although students are encouraged to choose a project relevant to their thesis research.

Recent research articles in the area of atomistic modeling will be discussed, with each student leadong a discussion of a recent research paper. Students will learn to assess the quality and significance of published computational results.


Topics that will be covered include:

Term project

Objective: To get experience in designing and performing computer simulations.

Parts of the project:

  1. Design (or adapt an idea from literature) a simulation that is of scientific or computational interest to you
  2. Choose and justify a computational approach appropriate for the problem of interest
  3. Write the code (or parts of the code that have not been supplied)
  4. Run simulations and analyze the results
  5. Prepare a report; include electronic copies of your code
  6. Present your results to the class (mini-symposium)
February 4th - have project approved by instructor
March 3rd - turn in introduction and discuss progress with instructor (optional)
May 8th - turn in research paper; give a presentation to the class at a mini-symposium

Tentative program of the mini-symposium can be found here

A set of example problems for term projects can be found here.

Projects: A problem chosen for the term project should have some science content and be doable in the timeframe of one semester. Students are encouraged to choose a project relevant to their thesis research. If the intention is to continue computational work in the future, the term project may be a well-defined part of a larger research project.

Discussion of published research articles

Each student will lead a discussion of a recent research paper in the area of atomistic simulations (~10-15 min). Papers will be posted at least one week before the discussion.

Title Author(s) Source Discussion Leader Day
Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways K. J. Kohlhoff, D. Shukla, M. Lawrenz, G. R. Bowman, D. E. Konerding, D. Belov, R. B. Altman, V. S. Pande Nature Chemistry 6, 15-21 (2014), link Jennifer Hays Thursday, March 17
Detailed atomistic simulation of a polymer melt/solid interface: Structure, density, and conformation of a thin film of polyethylene melt adsorbed on graphite K. Ch. Daoulas, V. A. Harmandaris, V. G. Mavrantzas Macromolecules 38, 5780 (2005), link Ben Canty Thursday, March 24
Molecular dynamics simulation of the contact angle of liquids on solid surfaces B. Shi, V. K. Dhir J. Chem. Phys. 130, 034705 (2009), PDF (268 kB) Qingchang Liu Tuesday, March 29
Thermal conductivity and phonon transport in empty and water-filled carbon nanotubes J. A. Thomas, R. M. Iutzi, and A. J. H. McGaughey Phys. Rev. B 81, 045413 (2010), link Yuan Gao Tuesday, April 12
Interfacial thermal conductance between silicon and a vertical carbon nanotube M. Hu, P. Keblinski, J.-S. Wang, and N. Raravikar J. Appl. Phys. 104, 083503 (2008), PDF (458 kB) Matt Barone Thursday, April 14
Comparison of atomic-level simulation methods for computing thermal conductivity Patrick K. Schelling, Simon R. Phillpot, and Pawel Keblinski Phys. Rev. B 65, 144306 (2002), link Rouzbeh Rastgar Tuesday, April 19
Atomic-level characterization of the structural dynamics of proteins D.E. Shaw, P. Maragakis, K. Lindorff-Larsen, S. Piana, R.O. Dror, M.P. Eastwood, J.A. Bank, J.M. Jumper, J.K. Salmon, Y. Shan, W. Wriggers Science 330, 341 (2010), PDF (2.6 MB) Alexander Yang Thursday, April 21
Predicting phonon dispersion relations and lifetimes from the spectral energy density J.A. Thomas, J.E. Turney, R.M. Iutzi, C.H. Amon, A.J.H. McGaughey Phys. Rev. B 81, 081411(R) (2010), link Jeffrey Braun Tuesday, April 26
Molecular dynamics simulation of reversibly self-assembling shells in solution using trapezoidal particles D.C. Rapaport Phys. Rev. E 86, 051917 (2012), link Zhongmin Zhang Tuesday, May 3
Actuation of a suspended nano-graphene sheet by impact with an argon cluster N. Inui, K. Mochiji, K. Moritani Nanotechnology 19, 505501 (2008), PDF (820 kB) Yue Zhang Tuesday, May 3
Plastic flow localization in irradiated materials: a multiscale modeling approach T. Diaz de la Rubia, H. M. Zbib, T. A. Khraishi, B. D. Wirth, M. Victoria, M. J. Caturla Nature 406, 871 (2000), PDF (413 Kb) Robert Klein Tuesday, May 3
Social force model for pedestrian dynamics Dirk Helbing and Péter Molnár Phys. Rev. E 51, 4282 (1995), link Chester Szwejkowski Tuesday, May 3

"The purpose of computation is insight, not numbers."
        Richard Hamming     Computational Materials Group     Materials Science & Engineering