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_ __What is Molecular Modeling?__
 Table of Contents
  Introductory Comments
  What is Molecular Modeling?
  Why is Molecular Modeling Important?
  What do some common molecules look like?
  Where's the Math?
  Carbon 3 Ways
  Carbon Compounds
  Water and Ice
  Water and Ice pt.II
  How to view structures in class or at home
  MathMol Library of Structures.
  Tutorial 1: 1-Dimension, 2-Dimensions, 3-Dimensions...
  Tutorial2: The Geometry of 2 Dimensions..
  Tutorial3: The Geometry of 3- Dimensions
  Tutorial4: The Geometry of Molecules.
  Appendix1: Scientific Notation
  Appendix 2: Mass
  Appendix3: Volume
  Appendix4: Density
PT 2.

Below is a picture of a fatty acid protein molecule. The molecule oleic acid is bound inside the protein. The system contains thousands of atoms. A computer simulation was performed over of a period of 100 picoseconds to demonstrate the dynamic motion of the system. To perform this simulation took several days.

Shown are the backbone structure of the protein, a bound fatty acid molecule within the protein, and a small shell of water surrounding the protein. The time for the simulation was 100 picoseconds. The graphs give information about the motion of the lipid inside the protein.

To view the flash animation click the right mouse button while holding the cursor over image-->>click and play to start, then stop motion...

The simulation shows that molecules are not static but are in constant motion. There are many different kinds of motion within a molecule. We will discuss some of these motions in later sections.


Why is Molecular Modeling Important?____


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