A bias voltage by itself doesn't make sense, since there must be a reference terminal as well. Unless you are talking about a gate, but in that case the question still becomes, what are source and drain?
Also physically, you would never be able to separate a gate gap that only acts on the dielectric and not the hhhh atoms in the right electrode.
So, please consider what you really want to simulate - and since you ask about "transport", do indicate source and drain as well.
Or maybe I just didn't understand your drawing... You said "bias voltage on central region", which I would understand as a gate, which is consistent with your "bias voltage" arrows, but then the picture should be
----------------------> Z-direction
X-direction
| (bias-voltage) |
v v
********************
**** dielectric ****
********************
(hhhhhhhhhhhhhhhhhhh) hhhhhhhhhhhhhhhhhhhhhhh /\
(hhhhhhhhhhhhhhhhhhh) hhhhhhhhhhhhhhhhhhhhhhh |
(hhhhhhhhhhhhhhhhhhh) hhhhhhhhhhhhhhhhhhhhhhh |
hhhhhhhhhhhhhhhhhhhhhhh (hhhhhhhhhhhhhhhhhhhhhh) |
Left electrode hhhhhhhhhhhhhhhhhhhhhhh (hhhhhhhhhhhhhhhhhhhhhh) |
hhhhhhhhhhhhhhhhhhhhhhh (hhhhhhhhhhhhhhhhhhhhhh) |
Center region right electrode
If that's what you mean, then the answer is a clear "yes", ATK can treat this; in fact, it's basically identical in nature to
http://quantumwise.com/documents/tutorials/latest/GrapheneDevice/index.html/.