I did a blog post showing how to use UART4 to talk to an ATmega328p
[1]. My ATmega was at 3.3V though, so you'll need to use logic level
converters (MOSFETs) to convert between your 5V micro and the Beagle,
which operates at 3.3V logic levels. This blog post [2] uses the 5V
version and shows how to use the logic level converters.

If you have a recent debian image, you can enable UART 4 with the
following command:

echo BB-UART4 | sudo tee /sys/devices/bone_capemgr.*/slots

If you don't have the BB-UART4-00A0.dtbo in /lib/firmware, you should
probably upgrade your BBB.

After that command, you should see /dev/ttyO4 appear, which is the UART
you seek.

You may need to change the baud rate of your serial line, do that with
this command:

sudo stty -F /dev/ttyO4 9600

Good luck,

Josh


[1] http://datko.net/2013/11/11/bbb_atmega328p/
[2] 
http://www.instructables.com/id/Program-an-Arduino-using-BeagleBone-without-USB/?ALLSTEPS

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