Priye, Aashish (2015-05). Micro-Scale Complex Flows Enables Robust DNA Replication, Enhanced Transport and Tunable Fluid-Particle Interactions. Doctoral Dissertation. Thesis uri icon

abstract

  • The ability of convective flows in micro-scale confinement to direct chemical processes along accelerated kinetic pathways has been recognized for some time. However, practical applications have been slow to emerge because optimal results are often counterintuitively achieved in flows that appear to possess undesirably high disorder. Here we investigate the nature of these thermal instability driven Rayleigh-B?nard convective flows by altering the Rayleigh number and geometry of the cylindrical enclosure and thus identifying the chaotic flow regime. We then assess the ability of these flows to replicate DNA through polymerase chain reaction (PCR) across a broad ensemble of geometric states. The resulting parametric map reveals an unexpectedly wide chaotic regime where reaction rates remain constant over 2 orders of magnitude of the Rayleigh number, enabling robust convective PCR.

    With the new optimal design rules, we engineer a rugged, ultra-portable (300 g), inexpensive (<$20) bioanalysis platform for rapid nucleic acid-based diagnostics. The isothermal convective isothermal PCR format enables low power operation (5 V USB source). Time-resolved fluorescence detection and quantification is achieved using a smart-phone camera and integrated image analysis app. These advancements make it possible to provide gold standard nucleic acid-based diagnostics to remote field sites using consumer class quad-copter drones.

    The surprising interplay between reactions and micro-scale convective flows led us to consider adaptations beyond PCR. Specifically, we demonstrate that such flows, naturally established over a broad range of hydrothermally relevant pore sizes, function as highly efficient conveyors to continually shuttle molecular precursors from the bulk fluid to targeted locations on the solid boundaries, enabling greatly accelerated chemical synthesis. Insights from this study has the potential to provide a breakthrough in our understanding of the fundamental biochemical processes underlying the origin of life.

    The phenomenon of particle resuspension plays a vital role in numerous fields and thus an accurate description and formulation of van der Waals (vdW) interactions between the particle and substrate is of utmost importance. An approach based on Lifshitz continuum theory has been developed to calculate the principal many body interactions between arbitrary geometries at all separation distances to a high degree of accuracy. The new formulation can now provide realistic interactions for various particle-substrate systems which can then be coupled with computational fluid dynamics (CFD) models to improve the predictive capabilities of particle resuspension dynamics.

    Finally, We analyze trajectories of micro sized particles subject to all relevant hydrodynamic forces and torques by coupling discrete element modeling with CFD. The results provide us with important design rules to construct membraneless microfluidic filtration channels where pressure driven transverse flows and curvature induced dean flows can be simultaneously harnessed to assist size based particle separation with high throughput.

publication date

  • May 2015