Molecular Modeling and Theory
ChEg 698D
Spring, 2000 MWF 9:35-10:25, DBRT 207
Prof. Edward J. Maginn
Department of Chemical Engineering
University of Notre Dame
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Course Description
This course is intended mainly for graduate students and advanced undergraduates in chemical engineering. It is also appropriate for students with backgrounds in physics, chemistry or other fields that can make use of statistical mechanics, molecular theory and molecular simulation.
The course will be divided into roughly three parts. In the first part, we will cover elementary concepts in statistical mechanics and ensemble theory. In the second part, we will go over basic elements of classical molecular simulations, focusing on energy minimization, molecular dynamics and Monte Carlo methods. In the last part of the class, we will cover concepts from molecular theory. The exact topics covered during this part of the course will depend to some extent on the interests of the class, with mean field theories, transition state theory and integral equation theory being candidates.
Textbook
The required text for the course is "Molecular Modelling: Principles and Applications", Andrew R. Leach, Addison Wesley Longman, 1996. This book is available at the bookstore. We will loosely follow this book, but it does not contain adequate treatment of all the topics we will cover in class. There are also several books on reserve in the Engineering Library that you will want to consult over the course of the semester:
Prerequisites
It is assumed that you have a good basic understanding of thermodynamics, physical chemistry and mathematics (up through and including differential equations). Knowledge of statistical and quantum mechanics is not necessary but would be helpful. We will review the essential features of statistical mechanics necessary to conduct basic molecular simulations. You will be required to do some amount of programming (in whatever language you choose) and should be able to read and understand code. We may be able to provide you software as templates for your projects, but they will be primarily in Fortran or C. Good reference materials are on reserve in the Engineering Library. If you do not have basic programming skills and feel as though you will need some extra help, come talk to me and I will try to help you get up to speed.
Grading, Exams and Homework
There will be one take home exam around the mid-point of the class. Homework assignments will be due periodically over the semester. A final project along with an in-class presentation will be due at the end of the course. The exam, homework and final project/presentation each make up 1/3 of the grade for the class.
I will say more about the final project later, but I would like for each student to work on a project using the concepts we've discussed in this course. You should come up with a problem in consultation with me. The problem can be anything of interest to you. Most people choose something related to their research, which I encourage. At the end of the course, each student will make an in-class presentation of their project to the rest of the class.
Contact Information
I will not have scheduled office hours, but will be free to meet with you anytime to discuss the class. I prefer if you schedule a meeting with me ahead of time. You can do this via email. My contact information is
Prof. Edward Maginn, 176 Fitzpatrick Hall.