MSE485/PHYS466/CSE485 :: MatSE Illinois :: University of Illinois at Urbana-Champaign



We will be using i>clickers in every lecture. You can use either the older v1 or the newer v2 i>clickers. If you have not already done so, please register your clicker by visiting the MSE485 page in Compass. The navigation bar on the left should have an item "Register my i>clicker". The proven, educational benefit of using i>clickers depends on your active participation. Having another student answer questions using your clicker is considered cheating.

Online discussion forum

This class uses Piazza for announcements, updates, and all communication between the instructor, TAs, and students. Please visit this page to register.

Excused Absences

Excused absences may be requested by filling out the Excused Absences form. For more information, please read the course syllabus.


All lectures will be recorded and the recordings will be posted under this link.

Date Reading Description Assignment due
Tue Aug 29 Orientation and Introduction, Statistics I
Thu Aug 31 Old lecture notes, Frenkel Smit (Chapter 4 and Appendix D), LeSar (Appendix G) Statistics and Errors
Tue Sep 5 Old lecture notes, Frenkel Smit (Chapter 2), LeSar (Appendix D, G) Correlation, Bias, Python, iPython Notebook Statistics Errors
Thu Sep 7 Old lecture notes, Frenkel Smit (Chapter 2), LeSar (Appendix D, G) Statistical Mechanics
Tue Sep 12 Molecular Dynamics: Boundary conditions, Measuring
Thu Sep 14 Old lecture notes 1, Old lecture notes 2, Frenkel Smit (Chapter 4), LeSar (Chapter 3) Molecular Dynamics: Forces, Time propagation HW1 due 9/18 (upload here)
Tue Sep 19 Old lecture notes, Frenkel Smit (Appendix F), LeSar (Chapter 5) Molecular Dynamics: Code, Force fields
Thu Sep 21 Old lecture notes, Frenkel Smit (Chapter 4, Appendix F), LeSar (Chapter 5) Molecular Dynamics: Force fields II
Tue Sep 26 Old lecture notes, Frenkel Smit (Chapter 4), LeSar (Chapter 5) Molecular Dynamics: Potentials III
Thu Sep 28 Old lecture notes Pair correlation function HW2 (code) due 9/29 (upload here)
Tue Oct 3 Old lecture notes I, Old lecture notes II, Frenkel Smit (Chapter 6, Appendix B, C, E), LeSar (Chapter 6) Linear response and correlations, iPython Notebook Fourier Interpolation
Thu Oct 5 Old lecture notes I, Old lecture notes II, Frenkel Smit (Chapter 6, Appendix B, C, E), LeSar (Chapter 6) Thermostats
Tue Oct 10 Random Numbers and Random Number Generators
Thu Oct 12 Tests for Random Number Generators HW3 due 10/13 (upload here)
Tue Oct 17 Old lecture notes Non-uniform distribution
Thu Oct 19 Old lecture notes I, Old lecture notes II, Old lecture notes III, Old lecture notes IV, Frenkel Smit (Chapter 3), LeSar (Chapter 7) Variance reduction
Tue Oct 24 Old lecture notes, Frenkel Smit (Chapter 3) Metropolis Monte Carlo
Thu Oct 26 Old lecture notes, Frenkel Smit (Chapter 13, 17) Monte Carlo Dynamics HW4 due 10/27 (upload here)
Tue Oct 31 Old lecture notes, Frenkel Smit (Chapter 8), LeSar (Chapter 9) Kinetic Monte Carlo
Thu Nov 2 Old lecture notes I, Article, LeSar (Chapter 7) First-principles KMC, Ising model
Tue Nov 7 Old lecture notes, Frenkel Smit (Chapter 7, 11) Widom and Bennett method status report draft due (upload here)
Thu Nov 9 FS: Chapter 15 Constraints in MD HW5 due 11/10 (upload here); status report peer review due (11/13)
Tue Nov 14 Constraints; Polymers
Thu Nov 16 Project proposals status report final due
Tue Nov 21 Thanksgiving Break
Thu Nov 23 Thanksgiving Break
Tue Nov 28 Density Functional Theory HW6 due 12/1 (upload here)
Thu Nov 30 Visualizing Crystal Structures in Ovito (Hands-on)
Tue Dec 5 Old lecture notes Polymers; Quantum simulations
Thu Dec 7 Quantum Monte Carlo
Tue Dec 12 Special Topic: Crystal-Structure Prediction
Thu Dec 14 Reading Day final report draft due (12/13, 11.59 pm); peer review due (12/16, 11.59 pm); final report due (12/18, 11.59 pm)
Mon Dec 18, 8-11, 218 Ceramics FINAL: Presentations final presentations (send by 7.30 am)

Course Description


This class covers computer simulations on atomistic length and time scales for (structural or thermodynamic) properties of materials, numerical algorithms, and systematic and statistical error estimations. Concepts of statistical mechanics such as phase space and averages are critically important for this class. Students will become familiar with popular techniques to sample phase space, such as molecular dynamics (integration algorithms, static and dynamic correlations functions, and their connection to order and transport) and Monte Carlo and Random Walks (variance reduction, Metropolis algorithms, kinetic Monte Carlo, heat diffusion, Brownian motion). Example applications will include phase transitions (melting-freezing, calculating free energies) and polymers (growth and equilibrium structure). In addition, quantum simulations (zero temperature and finite temperature methods) and optimization techniques (e.g. simulated annealing) will be discussed.


The objective is to learn and apply fundamental techniques used in (primarily classical) simulations in order to help understand and predict properties of microscopic systems in materials science, physics, chemistry, and biology. Students will work towards a final project, where they will define, model, implement, and study a particular problem using atomic-scale simulation techniques. Use of the Python programming language, writing of proper reports, and presentation of results are important components of this class.

Course Grading


Your final grade for this class will be based upon your total score on all the components of the course. Please consult the course syllabus for details on particular components.

Course Component Percentage of total
In-lecture i>clicker10
Project Proposal10
Final Presentation15
Final Report15

Final Grade

The following cutoff table will be used to calculate final scores.

Final Grade Minimum Points
A+ 97
A 93
A– 90
B+ 87
B 83
B– 80
C+ 77
C 73
C– 70
D+ 67
D 63
D– 60
F <60