Numerical modeling of DNA-chip hybridization with chaotic advection

We present numerical simulations of DNA-chip hybridization, both in the static and dynamical cases. In the static case, transport of free targets is limited by molecular diffusion; in the dynamical case, an efficient mixing is achieved by chaotic advection, with a periodic protocol using pumps in a rectangular chamber. This protocol has been shown to achieve rapid and homogeneous mixing. We suppose in our model that all free targets are identical; the chip has different spots on which the probes are fixed, also all identical, and complementary to the targets. The reaction model is an infinite sink potential of width d(h), i.e., a target is captured as soon as it comes close enough to a probe, at a distance lower than d(h). Our results prove that mixing with chaotic advection enables much more rapid hybridization than the static case. We show and explain why the potential width d(h) does not play an important role in the final results, and we discuss the role of molecular diffusion. We also recover realistic reaction rates in the static case. (C) 2013 AIP Publishing LLC.