  Engineering molecular systems that exhibit complex behavior requires the
design of kinetic barriers. For example, an effective catalytic pathway must
have a large barrier when the catalyst is absent. While programming such energy
barriers seems to require knowledge of the specific molecular substrate, we
develop a novel substrate-independent approach. We extend the
recently-developed model known as thermodynamic binding networks, demonstrating
programmable kinetic barriers that arise solely from the thermodynamic driving
forces of bond formation and the configurational entropy of forming separate
complexes. Our kinetic model makes relatively weak assumptions, which implies
that energy barriers predicted by our model would exist in a wide variety of
systems and conditions. We demonstrate that our model is robust by showing that
several variations in its definition result in equivalent energy barriers. We
apply this model to design catalytic systems with an arbitrarily large energy
barrier to uncatalyzed reactions. Our results could yield robust amplifiers
using DNA strand displacement, a popular technology for engineering synthetic
reaction pathways, and suggest design strategies for preventing undesired
kinetic behavior in a variety of molecular systems.
