1. COS 126 – Atomic Theory of Matter

2. Announcements Project – due Friday (1/12) midnight TA Office Hours this week (check website) Lab Help (Mon-Fri 7pm-9pm) Output should EXACTLY match examples Can use Diff.java (9.6) Start early…. Exam 2 – Pickup from your TA

3. Atomic Theory Overview Brownian Motion Random collision of molecules Displacement over time fits a Gaussian distribution

4. Atomic Theory Overview Avogadro’s Number Number of atoms needed to equal substances atomic mass in grams N A atoms of Carbon-12 = 12 grams Can calculate from Brownian Motion Variance of Gaussian distribution is a function of resistance in water, number of molecules

5. Bead.java Represent particles (beads) in water API public Bead() public void add(int i, int j) public int mass() // number of pixels public double distanceTo(Bead b) // from center (average) public String toString() Only need 3 values to efficiently store Thoroughly test (simple main)

6. BeadFinder.java Locate all beads in a given image API public BeadFinder(Picture picture, double threshold) Calculate luminance (see Luminance.java, 3.1) Count pixels with at luminance > threshold Find beads with DFS (see Percolation.java, 2.4) The hard part, next slide… public Bead[] getBeads(int minSize) Returns all beads with at least minSize pixels Array must be of size equal to number of beads

7. Bead Finder - Depth First Search Use boolean[][] array to mark visited Traverse image Dark pixel – mark as visited, continue Light pixel – create new bead, call dfs DFS algorithm If pixel out-of-bounds, return If pixel has been visited, return If pixel is dark, mark + return Add pixel to current bead, mark as visited Recursively visit up, down, left, right

8. Bead Finder - Depth First Search Use boolean[][] array to mark visited Traverse image Dark pixel – mark as visited, continue Light pixel – create new bead, call dfs DFS algorithm If pixel out-of-bounds, return If pixel has been visited, return If pixel is dark, mark + return Add pixel to current bead, mark as visited Recursively visit up, down, left, right

9. Bead Finder - Depth First Search Use boolean[][] array to mark visited Traverse image Dark pixel – mark as visited, continue Light pixel – create new bead, call dfs DFS algorithm If pixel out-of-bounds, return If pixel has been visited, return If pixel is dark, mark + return Add pixel to current bead, mark as visited Recursively visit up, down, left, right

10. Bead Finder - Depth First Search Use boolean[][] array to mark visited Traverse image Dark pixel – mark as visited, continue Light pixel – create new bead, call dfs DFS algorithm If pixel out-of-bounds, return If pixel has been visited, return If pixel is dark, mark + return Add pixel to current bead, mark as visited Recursively visit up, down, left, right

11. Bead Finder - Depth First Search Use boolean[][] array to mark visited Traverse image Dark pixel – mark as visited, continue Light pixel – create new bead, call dfs DFS algorithm If pixel out-of-bounds, return If pixel has been visited, return If pixel is dark, mark + return Add pixel to current bead, mark as visited Recursively visit up, down, left, right

12. Bead Finder - Depth First Search Use boolean[][] array to mark visited Traverse image Dark pixel – mark as visited, continue Light pixel – create new bead, call dfs DFS algorithm If pixel out-of-bounds, return If pixel has been visited, return If pixel is dark, mark + return Add pixel to current bead, mark as visited Recursively visit up, down, left, right

13. BeadTracker.java Track beads between successive images Single main function Take in a series of images Output distance traversed by all beads for each time-step For each bead found at time t+1, find closest bead at time t and calculate distance Not the other way around! Don’t include if distance > 25 pixels (new bead)

14. Avogadro.java Analyze Brownian motion of all calculated displacements Lots of crazy formulas, all given, pretty straightforward Be careful about units in the math, convert pixels to meters, etc.

15. Random Thoughts… BeadTracker and Avogadro are separate clients, must recompile both Can still do Avogadro without other parts working, use sample input Only keep at most two pictures open at a time (run out of memory otherwise) Output format - System.out.printf() "%6.3f" -> _2.354 "%10.4e" -> 1.2535e-23

16. Announcements Project – due Friday (1/12) midnight TA Office Hours this week (check website) Lab Help (Mon-Fri 7pm-9pm) Output should EXACTLY match examples Can use Diff.java (9.6) Start early…. Exam 2 – Pickup from your TA