Before revision:  Our simulations exhibit non-ideal behaviour as expected in an experimental implementation of strand displacement operations. We characterize this non-ideal behaviour in detail and characterize how the kinetic operation of the gate depends on the  toehold and adjacent domain lengths.
After revision:  Our simulations exhibit non-ideal effects due to transient bubbles revealing undesired toeholds and thermal melting of whole strands. We have also characterized the bound and unbound kinetics of single strands, and in particular the kinetics of the total AND operation and the toehold and adjacent domain lengths.