1. Accurate 3D Modeling of User Inputted Molecules Using a Nelder Mead Algorithm
Ben Parr
Period 6

2. Introduction
Create program to let users easily and intuitively create simple molecules (i.e. not macromolecules)‏
Water (H2O)‏
Benzene (C6H6)‏
Nicotine (C10H14N2)‏
Have the program position the atoms correctly
Easy viewing for a better understanding of the geometry of molecules

3. Background
Understanding the geometry of molecules is extremely helpful
Buying molecule modeling sets for every student in an introductory chemistry is too costly
Some software similar to my project is also costly
No real feasible option for beginner chemistry students

4. Current State All graphics and user interface implemented
Nelder Mead Algorithm programmed

6. Nelder Mead Algorithm Start with original simplex
Has N+1 vertices where N = 3 * (# of atoms in model)‏
Multiply by 3 because each atom has a x, y, z
Each vertex has 3*N dimensions (contains the x,y,z of each atom in the model)‏
Used to minimize an energy function
“energy” of the model
Run through the algorithm until the tolerance (max energy of vertex – min energy of vertex) is less than

7. One Possible Variation

8. What's Next Program energy function that takes into account:
The distance between atoms (maximize)‏
The distance between bonded atoms
Make them a defined distance away from each other (values from a text file)‏
Create a better original simplex
Current original simplex is just for testing purposes
Too small may lead to local search
Too large could take too long