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University of Virginia, Department of Materials Science and Engineering Fall 2009, Tuesday and Thursday, 12:30-13:45 Wilsdorf Hall, Room 101 | |
about the corresponding projects |
MSE 4592/6270: 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: 09f-mse-4592-6270@collab.itc.virginia.edu |
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Homework #1 was due Tuesday, September 8 Homework #2 was due Thursday, September 24 Homework #3 was due Tuesday, October 13 Homework #4 was due Thursday, October 22 Homework #5 was due Tuesday, November 10 |
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:
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 for discussion
| Title | Author(s) | Source | Discussion Leader | Day |
| 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) | Bing Hao | October 29 |
| Diffusion of nanoclusters | P. Jensen, A. Clement, L. J. Lewis | Computational Materials Science 30, 137-142 (2004), PDF (422 Kb) | Qiang Qian | November 10 |
| Atomistic simulation of an f.c.c./b.c.c. interface in Ni-Cr alloys | J. K. Chen, D. Farkas and W. T. Reynolds Jr | Acta Materialia 45, 4415 (1998), PDF (515 Kb) | Xiaowei Liu | November 12 |
| Amorphization and Fracture in Silicon Diselenide Nanowires: A Molecular Dynamics Study | W. Li, R. K. Kalia, P. Vashishta | Phys. Rev. Lett. 77, 2241 (1996), PDF (228 kB) | Wenjing Yin | November 17 |
| Microscopic view of structural phase transitions induced by shock waves | K. Kadau, T. C. Germann, P. S. Lomdahl, B. L. Holian | Science 296, 1681 (2002), PDF (994 kB) | Harmonie Sahalov | November 19 |
| Calculations of the thermal conductivities of ionic materials by simulation with polarizable interaction potentials | N. Ohtori, M. Salanne, P. A Madden | J. Chem. Phys. 130, 104507 (2009), PDF (334 kB) | Theron Rodgers | November 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) | Hui Xu | November 24 |
| Multiscale modeling approach for calculating grain-boundary energies from first principles | O. A. Shenderova, D. W. Brenner, A. A. Nazarov, A. E. Romanov, L. H. Yang | Phys. Rev. B 57, R3181 (1998), PDF (110 kB) | Priya Ghatwai | December 1 |
| Molecular dynamics study of self-diffusion in bcc Fe | M. I. Mendelev, Y. Mishin | Phys. Rev. B 80, 144111 (2009), PDF (578 kB) | Chengping Wu | December 1 |
| Drag on a nanotube in uniform liquid argon flow | W. Tang and S. G. Advani | J. Chem. Phys. 125, 174706 (2006), PDF (751 Kb) | David Nicholson | December 3 |
| Brine rejection from freezing salt solutions: A molecular dynamics study | L. Vrbka, P. Jungwirth | Phys. Rev. Lett. 95, 148501 (2005), PDF (1.2 Mb) | Jukka-Pekka Kaikkonen | December 3 |
| Molecular dynamics simulation of the thin film deposition of Co/Cu(111) with Pb surfactant | B.-H. Kim and Y.-C. Chung | J. Appl. Phys. 106, 044304 (2009), PDF (355 Kb) | Qiaohua Tan | December 8 |
| Connecting atomistic and mesoscale simulations of crystal plasticity | V. Bulatov, F. F. Abraham, L. Kubin, B. Devincre, S. Yip | Nature 391, 669 (1998), PDF (429 Kb) | ||
| 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) | ||
| Low-speed fracture instabilities in a brittle crystal | J. R. Kermode, T. Albaret, D. Sherman, N. Bernstein, P. Gumbsch, M. C. Payne, G. Csanyi, A. De Vita | Nature 455, 1224 (2008), PDF (713 Kb) | ||
| 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) | ||
| Microscopic insights into the sputtering of thin organic films on Ag{111} induced by C60 and Ga bombardment | Z. Postawa, B. Czerwinski, N. Winograd, and B. J. Garrison | J. Phys. Chem. B 109, 11973 (2005), PDF (983 kB) | ||
| How Fast Can Cracks Propagate? | F. F. Abraham & H. Gao | Phys. Rev. Lett. 84, 3113 (2000), PDF (144 kB) | ||
| Dynamics of nanoscale jet formation and impingement on flat surfaces | S. Murad and I. K. Puri | Physics of Fluids 19, 128102 (2007), PDF (697 kB) | ||
| Molecular dynamics study of martensitic transformations in sintered Fe-Ni nanoparticles | K. Kadau, P. Entel, and P. S. Lomdahl | Comp. Phys. Commun. 147, 126-129 (2002), PDF (715 Kb) | ||
| 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) | ||
| Molecular dynamics study of solid thin-film thermal conductivity | J. R. Lukes, D. Y. Li, X.-G. Liang, C.-L. Tien | Journal of Heat Transfer 122, 536-543 (2000), PDF (624 Kb) | ||
| Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing | V. S. Pande, I. Baker, J. Chapman, S. P. Elmer, S. Khaliq, S. M. Larson, Y. M. Rhee, M. R. Shirts, C. D. Snow, E. J. Sorin, B. Zagrovic | Biopolymers 68, 91-109 (2003), PDF (746 Kb) Also see this link |
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| Changing Shapes in the Nanoworld | N. Combe, P. Jensen and A. Pimpinelli | Phys. Rev. Lett. 85, 110-113 (2000), PDF (260 kB) | ||
| 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) | ||
| Experiment and simulation of cluster emission from 5 keV Ar > Cu | T. J. Colla, H. M. Urbassek, A. Wucher, C. Staudt, R. Heinrich, B. J. Garrison, C. Dandachi und G. Betz | Nucl. Instrum. Meth. B 143, 284-297 (1998), PDF (1 Mb) | ||
| 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) | ||
| Test of the Universal Scaling Law for the Diffusion Coefficient in Liquid Metals | J. J. Hoyt, M. Asta, B. Sadigh | Phys. Rev. Lett. 85, 594 (2000), PDF (85 kB) | ||
| A simple model for the growth of polycrystalline Si using the kinetic Monte Carlo simulation | S. W. Levine and P. Clancy | Modelling Simul. Mater. Sci. Eng. 8, 751 (2000), PDF (631 kB) | ||
| Diffusion limited biofilm growth | P. Gonpot, R. Smith and A. Richter | Modelling Simul. Mater. Sci. Eng. 8, 707 (2000), PDF (1 MB) | ||
| Mesoscopic scale simulation of dislocation dynamics in fcc metals: Principles and applications | M Verdier, M Fivel and I Groma | Modelling Simul. Mater. Sci. Eng. 6, 755 (1998), PDF (486 kB) | ||
| Multi-lattice Monte Carlo model of thin films | H. Huang and G.H. Gilmer | Journal of Computer-Aided Materials Design 6, 117 (1999), PDF (635 kB) |