title: Numerical modeling of DNA-chip hybridization with chaotic advection.
abstract: 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 dh , i.e., a target is captured as soon as it comes close enough to a probe, at a distance lower than dh . 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 dh 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.
authors.affiliation: LMFA, CNRS-Université de Lyon, École Centrale de Lyon-Université Lyon 1-INSA Lyon, École Centrale de Lyon, 36 avenue Guy de Collongue, 69134 Écully cédex, France.
authors.forename: Florence
authors.initials: F
authors.lastname: Raynal
authors.affiliation: LMFA, CNRS-Université de Lyon, École Centrale de Lyon-Université Lyon 1-INSA Lyon, École Centrale de Lyon, 36 avenue Guy de Collongue, 69134 Écully cédex, France.
authors.forename: Aurélien
authors.initials: A
authors.lastname: Beuf
authors.affiliation: LMFA, CNRS-Université de Lyon, École Centrale de Lyon-Université Lyon 1-INSA Lyon, École Centrale de Lyon, 36 avenue Guy de Collongue, 69134 Écully cédex, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Carrière