(224e) Mapping Chaotic Flow States in Microscale Rayleigh-Bénard Convection to Identify Regimes of Accelerated DNA Replication

We have previously shown that chaotic advection in micro-scale flow geometries can be harnessed to greatly enhance the rate of thermally activated biochemical reactions (e.g., the polymerase chain reaction (PCR)). Here we present a 3D analysis of coupled flow and reaction that provides a time-resolved mapping of the DNA replication process as it unfolds. Chemical reaction kinetics are incorporated into the 3D flow model, enabling us to obtain a measure of global DNA replication rate within the entire reactor volume, expressed in terms of a characteristic doubling time. Mass action kinetics were assumed for the denaturing, annealing, and extension steps. Annealing and extension were modeled as bimolecular reactions to capture the contribution of the primers and dNTPs. Reversibility of denaturing and annealing reactions was also taken into account. Reaction models of varying complexity were compared via addition of side reactions. individual stream traces were examined for different geometries, expressed in terms of their aspect ratio (height/diameter, h/d). The residence time of a fluid element in a particular reaction zone and the number of times that fluid elements pass through the zones were determined for 300 randomly chosen stream traces yielding a distribution of residence times and frequencies of ingress in each of the reaction zones. At larger values of h/d we find that individual fluid elements on average spend more time in each temperature zone. But the number of times a fluid element passes through each zone is much larger in wider geometries (lower h/d), owing to the chaotic characteristics of the flow field. Since our experiments show much faster DNA replication at low h/d, the number of excursions into each reaction zone appears to play a more important role than the transit time through each temperature range. Finally a reaction map was constructed to determine the cylindrical cell geometries and other parameters that should be used to enhance the efficiency of microscale Rayleigh Bénard convection PCR. These results highlight the importance of the flow field's 3D characteristics.