Issue with driving multiple LEDs via transistors
The article you referenced uses MOSFET transistors, not a BJT like the TIP31. The big difference is that a MOSFET is a voltage-triggered (high impedance) device while a BJT is current-triggered (low-impedance) device. The result of this is that with an NPN transistor, you need a series resistor to limit the current flowing from the arduino IO pin through the transistor base. Without this, you are likely to damage the Auduino and/or the transistor. Try putting a 510 ohm resistor between each source and base and remove the pulldown resistors.