1210.6156 (Carsten Svaneborg et al.)

Non-Ideality and Kinetics of a Strand Displacement AND Gate    [PDF]

Carsten Svaneborg, Harold Fellermann, Steen Rasmussen

We perform a spatially resolved simulation study of an AND gate based on DNA strand displacement. DNA strands are modelled using a coarse-grained dynamic bonding model [C. Svaneborg, Comp. Phys. Comm. 183, 1793 (2012)]. We simulate the operation of the AND gate using several lengths of the toehold and the adjacent domains. 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. In particular, we observe that, while the final output state is reached with high fidelity when both input strands are present, our simulations exhibit numerous long-lived transition paths from the initial input state to the final output state.

View original: http://arxiv.org/abs/1210.6156