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

TL;DR

This paper demonstrates how 3D chaotic flow patterns in micro-scale geometries can significantly accelerate DNA replication in convective PCR, with models predicting faster doubling times in wider geometries.

Contribution

It introduces a coupled 3D CFD and kinetic model to quantify the impact of chaotic flow on PCR efficiency, highlighting the importance of flow geometry.

Findings

Chaotic flow enhances DNA replication speed.

Wider geometries lead to lower doubling times.

Model predictions align with experimental data.

Abstract

Micro-scale flow in cylindrical geometries can harness chaotic advection to perform complex thermally activated biochemical reactions such as the polymerase chain reaction (PCR). We have applied a 3D computational fluid dynamics model to resolve the complex flow patterns in such geometries. The resulting 3D flow trajectories are then used as input to a kinetic model to resolve the time evolution of DNA replication process. A simple mass action kinetic model was developed to couple these biochemical reactions with the intricate flow. Residence time analysis of virtual particles in the flow revealed that the flow has a strong chaotic component in wider geometries in comparison with taller geometries (quasi periodic motion). This work shows, for the first time that the chaotic aspect of the flow field plays a key role in determining 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 are lower in wider geometries, in agreement with experimental results.