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Micro-scale flow in cylindrical geometries can harness chaotic advection toperform complex thermally activated biochemical reactions such as thepolymerase chain reaction (PCR). We have applied a 3D computational fluiddynamics model to resolve the complex flow patterns in such geometries. Theresulting 3D flow trajectories are then used as input to a kinetic model toresolve the time evolution of DNA replication process. A simple mass actionkinetic model was developed to couple these biochemical reactions with theintricate flow. Residence time analysis of virtual particles in the flowrevealed that the flow has a strong chaotic component in wider geometries incomparison with taller geometries (quasi periodic motion). This work shows, forthe first time that the chaotic aspect of the flow field plays a key role indetermining the strength of the coupling between the reactions and the flow.Our model can quantify the doubling times of these reactions capturing the lag,exponential and plateau phases of PCR. It predicts that doubling times arelower in wider geometries, in agreement with experimental results.

Selecting 3D Chaotic Flow States for Accelerated DNA Replication in Micro Scale Convective PCR