Methods of Computational Science

Look at the detailed syllabus for this course.

Instructors

Hiroshi Matsuoka
Office: Moulton Hall 313B
Phone: 438-3236
Office hours: 2 - 3 p.m. (MTWRF) or by appointment.

Jean Standard
Office: Felmley Hall 331A
Phone: 438-7700
Office hours: 10 a.m. - 12 p.m. (TR) or by appointment.

Texts:

Gregory L. Baker and Jerry P. Gollub, "Chaotic dynamics: an introduction," Cambridge University Press.

Harvey Gould and Jan Tobochnik, "Computer Simulation Methods, Applications to Physical Systems, Part 1 and Part 2," Addison-Wesley.

Rapid progress in computer technology in recent years has allowed both chemists and physicists to explore complex systems such as nonlinear chaotic dynamical systems and many body systems including macromolecules, liquids, glasses, and solids. Computational methods used in studies of these systems are now becoming an integral part of chemistry and physics.

It is therefore beneficial for those in chemistry and physics to acquire skills in applying these computational techniques to problems in their disciplines. Applied computer scientists are also increasingly involved in application of these techniques in both academic and industrial environments. It is then a definite advantage for those in applied computer science to be familiar with these computational methods.

The aim of this course is to help you (i.e., majors in Applied Computer Science, Chemistry, and Physics) learn how to solve problems in chemistry and physics through computer modeling and simulations. The course covers a variety of basic algorithms for numerical solution of Newton's equations of motion and chemical kinetics equations, molecular dynamics simulations, and Monte Carlo simulations. These computational techniques are introduced via specific applications to chemical and physical problems in order for you to develop the computational skills and scientific intuition required to tackle these problems.

Course Objectives

1. To understand how to approach problems in chemistry and physics by computer modeling and simulations of real systems.

2. To understand basic algorithms for numerical solution of Newton's equations of motion and chemical kinetics equations, molecular dynamics simulations of simple liquids and solids, and Monte Carlo simulations of phase transitions.

3. To be able to assess the advantages and disadvantages of each algorithm for problems in chemistry and physics.

4. To be able to implement these algorithms as computer programs.

5. To apply these algorithms to studies of specific chemical and physical systems.

6. To analyze the results produced by these algorithms by comparing with known analytical solutions and limiting cases, by applying scientific intuition, and through computer visualization.

References: Recommended references include the following:

1. William H. Press, Brian P. Flannery, Saul A. Teukolsky, and William T. Vetterling, "Numerical Recipes - The Art of Scientific Computing," Cambridge University Press.

2. Alejandro L. Garcia, "Numerical Methods for Physics," Prentice Hall.

3. Paul L. DeVries, "A First Course in Computational Physics," John Wiley & Sons, Inc.

4. Steven E. Koonin and Dawn C. Meredith, "Computational Physics Fortran Version," Addison-Wesley.

5. "Introduction to the ISU Physics Department Computer System", PIP Printing.

Homework

(1) A homework problem will be assigned usually as soon as a topic relevant to the problem is discussed in class.

(2) Present your solutions neatly and clearly. Illegible and/or disorganized solutions will not be graded.

(3) Solutions will be available in a file in the Physics Department office and in a case outside Felmley 333 in the Chemistry Department.

(4) Late homework will lose points every day, and will not be accepted after the solutions become available.

Hour Exams

(1) There will be 2 hour exams.

(2) No make-up exam will be given unless you can present an official proof for an uncontrollable circumstance such as serious illness of yourself or in your immediate family. An arrangement for a make-up exam must be made within one week after the exam. If you fail to do so, you will not be able to take a make-up exam.

Final Exam At 1:00 p.m. on Wednesday, May 10.

Grades:

Attendance, class participation, homework, and computer projects...55 %
2 Hour exams...30 %
Final exam...15%


Your final letter grade will be determined as follows:

A.............above 90 %
B.............above 80 %
C.............above 70 %
D.............above 60 %

Miscellaneous

January 30 (Monday): the last day to withdraw from the course with no withdrawal grade (WX).

February 17 (Friday): the last day to withdraw from the course with a WX grade.