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University of Virginia, Department of Materials Science and Engineering Fall 2011, Tuesday and Thursday, 20:00 - 21:15 Thornton Hall A, Room 119 | |
about the corresponding projects |
MSE 4270/6270: Introduction to Atomistic Simulations Instructor: Leonid V. Zhigilei Office: Wilsdorf Hall, Room 303D Office Hours: open Telephone: (434) 243 3582 E-mail: lz2n@virginia.edu Web: http://www.people.virginia.edu/~lz2n/mse627/ Class e-mail list: 11f-mse-4270-6270@collab.itc.virginia.edu |
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Homework #1 was due Tuesday, September 6 Homework #2 was due Thursday, September 22 Homework #3 was due Thursday, October 13 Homework #4 was due Thursday, October 27 Homework #5 was due Tuesday, November 15 Mini-symposium (presentation of term projects): 9:30 am - 4:00 pm, Friday and Saturday, December 9-10, 2011, MSE Building, Room 125 Tentative program of the mini-symposium can be found here |
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 presenting one or two article. Students will learn to assess the quality and significance of published computational results.
Topics that will be covered include:
Objective: To get experience in designing and performing computer simulations.
Parts of the project:
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 at least two discussions of a recent research paper in the area of atomistic simulations (~10-15 min). Although a few papers will be proposed by instructor, students are encouraged to propose papers that are interesting or relevant to their research work (but not to the term project). Papers will be distributed at least one week before the discussion.
Examples of research articles (from past discussions)
| Title | Author(s) | Source | Discussion Leader | Day |
| Multiple shear banding in a computational amorphous alloy model | M. Wakeda, Y. Shibutani, S. Ogata, J. Park | Appl. Phys. A 91, 281 (2008), PDF (400 kB) | Cheng-Yu Shih | Tuesday, October 18 |
| Molecular dynamics simulations of arbon nanotubes in water | J. H. Walther, R. Jaffe, T. Halicioglu, P. Koumoutsakos | Center for Turbulence Research, Proceedings of the Summer Program, pp. 5-20 (2010), PDF (402 kB) | Karen Long | Thursday, October 27 |
| Locally activated Monte Carlo method for long-time-scale simulations | M. Kaukonen, J. Peräjoki and R. M. Nieminen | Phys. Rev. B 61, 980 (2000), PDF (94 kB) | Xuhui Feng | Thursday, October 27 |
| Hierarchical models of plasticity: dislocation nucleation and interaction | R. Phillips, D. Rodney, V. Shenoy, E. Tadmor and M. Ortiz | Modelling Simul. Mater. Sci. Eng. 7, 769 (1999), PDF (990 kB) | Brad Richards | Thursday, October 27 |
| 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) | Jayaprakash Srinivasan | Tuesday, November 1 |
| A molecular dynamics study of the graphitization ability of transition metals for catalysis of carbon nanotube growth via chemical vapor deposition | Y. Shibuta, J.A. Elliott | Chem. Phys. Lett. 472, 200 (2009), PDF (2.2 MB) | Brandon McClimon | Thursday, November 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) | Rebecca Conti | Monday, November 7 |
| Molecular dynamics simulations of carbon nanotube-based gears | J. Han, A. Globus, R. Jaffe, G. Deardorff | Nanotechnology 8, 95 (1997), PDF (816 kB) | Bernard Wittmaack | Monday, November 7 |
| Photodesorption of water ice: A molecular dynamics study | S. Andersson, E.F. van Dishoeck | Astronomy and Astrophysics 491, 907 (2008), PDF (580 kB) | Micah Schaible | Monday, November 7 |
| Gallium-induced milling of silicon: A computational investigation of focused ion beams | M.F. Russo,Jr., M. Maazouz, L.A. Giannuzzi, C. Chandler, M. Utlaut, B.J. Garrison | Microsc. Microanal. 14, 315 (2008), PDF (390 kB) | Christopher Duska | Monday, November 7 |
| Molecular dynamics study of self-diffusion in bcc Fe | M. I. Mendelev, Y. Mishin | Phys. Rev. B 80, 144111 (2009), PDF (578 kB) | Thomas Lawlor | Monday, November 7 |
| Thermal transport in graphene and effects of vacancy defects | H. Zhang, G. Lee, K. Cho | Phys. Rev. B 84, 115460 (2011), PDF (660 kB) | Nam Le | Monday, November 7 |
| Pillared graphene: A new 3-D network nanostructure for enhanced hydrogen storage | G.K. Dimitrakakis, E. Tylianakis, G. E. Froudakis | Nano Lett. 8, 3166 (2008), PDF (2.1 MB) | Chris Baker | Monday, November 7 |
| 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) | Christoph Klein | Monday, November 7 |
| Simulation of the formation and morphology of ice mantles on interstellar grains | H.M. Cuppen, E. Herbst | Astrophys. J. 668, 294 (2007), PDF (700 kB) | Herbert Ryan | Monday, November 7 |
| Epitaxial growth of Si1-xGex on Si(100)2x1: A molecular-dynamics study | S. Ethier, L. J. Lewis | J. Mater. Res. 7, 2817 (1992), PDF (1.0 MB) | Gopalakrishnan Ramalingam | Thursday, November 10 |
| Molecular dynamics simulation of ice nucleation and growth process leading to water freezing | M. Matsumoto, S. Saito, I. Ohmine | Nature 416, 409 (2002), PDF (573 kB) | Kevin Duvall | Thursday, November 10 |
| Embedded-atom method: Derivation and application to impurities, surfaces, and other defects in metals | M. S. Daw, M. I. Baskes | Phys. Rev. B 29, 6443-6453 (1984), PDF (1.2 MB) | Jayendran Srinivasan | Tuesday, November 29 |
| Brine rejection from freezing salt solutions: A molecular dynamics study | L. Vrbka, P. Jungwirth | Phys. Rev. Lett. 95, 148501 (2005), PDF (1.2 Mb) | Tyler Owens | Thursday, December 1 |
| Molecular dynamics simulations of stress-induced phase transformations and grain nucleation at crack tips in Fe | A. Latapie and D. Farkas | Modelling Simul. Mater. Sci. Eng. 11, 745-753 (2003), PDF (1.2 Mb) | Jishnu Bhattacharyya | Thursday, December 1 |
| Extended Finnis-Sinclair potential for bcc and fcc metals and alloys | X.D. Dai, Y. Kong, J.H. Li, B.X. Liu | J. Phys.: Condens. Matter 18, 4527 (2006), PDF (740 kB) | Max Lupton | Thursday, December 1 |
| Interfacil thermal conductance between silicon and a vertical carbon nanotube | M. Hu., P. Keblinski, J.-S. Wang, N. Raravikar | J. Appl. Phys. 104, 083503 (2008), PDF (465 kB) | Justin Smoyer | Thursday, December 1 |