First, I chose the two basic colors I wanted in the nucleus part of the icon and made a gradient from the top of the project to the bottom.

Then I used a wave filter (Filter-Distort-Wave) to create an up and down pattern and then polarized it (Filter-Distort-Polar Coordinates-Rectangular to Polar).

Then I chose the section I wanted for the icon and messed with the color a bit by adding a circle the same size in the background and changing opacity.

Then I created two highlights for the top half of the nucleus and the bottom half. I also applied a few layer styles.

(The nucleus and two highlights are shown separately in the top right corner.)

Then, I used the pen tool to draw out the orbits (one is shown in the top right corner), chose a gray foreground color and a hard, 9px-diameter brush, and created a stroke on the path, using simulated pressure to make the orbit seem smaller as it went behind the nucleus. I also added some layer styles.

Then, I created another icon (shown in the top right corner) like the original nucleus. However, this one didn't use the starburst effect and was yellow with a slight glow behind it, created by gaussian blurring the yellow circle (main part of the icon).

I duplicated the yellow icon (electrons) and placed the icons around the orbits and erased certain parts of them to make it seem as though the orbit was passing through the center of each electron.

I then added a shadowy layer (shown in bottom left corner) on top of all of the layers to make the nucleus seem more round, erasing the parts that covered up orbits and electrons.