CZ1103: Introduction to Computational Science (1999)

Synopsis
An overview on computational science. Introductory topics in computing tools, computational mathematics, physics, chemistry and biology. Practical lab sessions on distinguished commercial softwares.

Instructor
Dr. Chen Yu Zong
Department of Computational Science
National University of Singapore
Office: Blk S17 Room 07-24
Tel: 6874-6877. Fax: 6774-6756
E-mail: yzchen@cz3.nus.edu.sg
Web: http://www.cz3.nus.edu.sg/~yzchen (Lots of info about biocomputing)

Teaching Assistant
Mr. Yung Shing Gene
Department of Computational Science
National University of Singapore
Office: Blk S17 Room 07-30
Tel: 6874-5214.
E-mail: shing@cz3.nus.edu.sg

Schedule

• Lectures:
  • Monday/Thursday 2:00-3:00pm, at LT22
• Labs:
  • Alternating weeks, at CZ 1st year lab and honour's lab. Starts after completing the introductory lab sessions. Time to be determined.
• Tutorials:
  • First tutorial starts in week 3. Time and location to be determined.
• Grade:
  • Final exam: 50%,
  • Mid-term exam: 20%,
  • Lab: 30%
• Exams:
  • One mid-term exam: Sept. 13, 1999 (Open Book).
  • One final exam: Nov. 10, 1999 (Close Book). Time: AM. Venue: Competition Hall (beside MPSH).

Module Outline
(Online documents for all of the lectures are available. Click on each item below to access the relevant document).

• Introduction.
  • Lecture  1: Introduction.
• Computational Tools
  • Lecture  2: MatLab.
  • Lecture  3: MatLab, part II.
• Computational Mathematics
  • Lecture  4: Mathematical modeling
  • Lecture  5: Analyzing scientific data.
  • Lecture  6: Chaos and dynamical systems.
    • (A remote on-line program).
  • Lecture  7: Fractals.
    • (On-line introduction about fractals).
• Computational Physics
  • Lecutre  8: Newton's law and planetary motions.
    1. Demo of Newton's law,
    2. Demo of planetary motions
  • Lecture  9: Molecular dynamics simulation.
    1. More detailed description of MD
    2. A Matlab program
    3. Demo of MD
       
  • Lecture 10: Potential, field, waves, and fluid flows.
    1. Demo of electric field,
    2. Field of a moving charge,
    3. Wave,
    4. Atmosphere flow).
• Computational Chemistry
  • Lecture 11 and 12: Chemical compounds and structure drawing software ISIS draw.
  • Lecture 13: Stereochemistry and 3D graphics software Rasmol.
  • Lecture 14: Molecular mechanics in chemistry.
• Computational Biology
  • Lecture 15-16: Molecules of life.
  • Lecture 17-18: Information and databases in molecular biology.
  • Lecture 19: Sequence alignment and internet tools.
  • Lecture 20: Homology based protein modeling.
  • Lecture 21: Computer aided drug design.
    

Lab Schedule

• Lab 1: Practical use of MatLab.
• Lab 2: Mathematical modeling and fractals.
• Lab 3: Newton's law and molecular dynamics.
• Lab 4: Building a chemical compound on computer.
• Lab 5: Internet access of biological information.
• Lab 6: Protein graphics.
  

Tutorials

• MatLab.
• Mathematical modeling.
• Computational physics.
• Computational chemistry.
• Computational biology.
  

A Note About Textbook
While its methods have been widely used in all aspects of science and technology, computational science as a scientific dicsipline is in an early stage of development. Currently there is no textbook that covers all major areas. As a result, we plan to use our own lecture notes to teach this module. These notes can be obtained from the first year Lab of our department. A list of content can be found by clicking here.

References:

• MatLab Primer. Kermit Sigman. CRC Press, 1994.
• Computational Physics. Nicholas J. Giordano. Prentice Hall, 1997.
• Computational Chemistry. Guy H. Grant and W. Graham Richards. Oxford University Press, 1995.
• Introduction to Computational Molecular Biology. Joao Carlos Setubal and Joao Meidanis. PWS Pub., 1997.
• Molecular Modeling: Basic Principles and Applications. Hans-Dieter Holtje and Gerd Folks. VCH, 1997.