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Trapping of DNA by Thermophoretic Depletion and Convection in FEMLAB

Trapping of DNA by Thermophoretic Depletion and Convection in FEMLAB. Pawel Drapala University of Washington. Background. Effects of temperature gradients on the migration of concentrate in solution Ludwig-Soret Effect (1856) Research at the Rockefeller University in New York

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Trapping of DNA by Thermophoretic Depletion and Convection in FEMLAB

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  1. Trapping of DNA by Thermophoretic Depletion and Convection in FEMLAB Pawel Drapala University of Washington

  2. Background • Effects of temperature gradients on the migration of concentrate in solution • Ludwig-Soret Effect (1856) • Research at the Rockefeller University in New York • Degree of thermophoretic depletion of DNA • Measurement of the thermal diffusion coefficient for DNA (Braun, 2002)

  3. Experimental Setup Infrared Laser Plasmid size DNA solution suspended in plastic container

  4. Experimental Results 13 mW 50 μm 400 μm

  5. Experimental Results 27% increase in DNA concentration at the bottom edge. Can we model this experiment in FEMLAB?

  6. Theory • Convective Instability • buoyancy forces overcome the viscous drag forces of the fluid • fluid near the heat source expands, becomes less dense and rises to the top • Thermophoresis • Diffusion of DNA down temperature gradient • non-equilibrium thermodynamics couples the energy equation and the diffusivity equation by the use of phenomenological coefficients (deGroot, 1962)

  7. Governing Equations • Incompressible Navier-Stokes Equation • The Energy Equation • The Diffusivity Equation

  8. Non-dimensional Numbers • Grashoff number • Prandtl number • Schmidt number • Soret number • Power number

  9. Model Geometry

  10. Model Geometry

  11. Model Geometry Axi-Symmetric Boundary Condition Insulation and No Slip Boundary Condition

  12. Mesh Statistics Number of Degrees of Freedom: 17487 Number of Elements: 2008 Number of Boundary Elements: 68

  13. Temperature Profile Results

  14. Velocity Profile Results

  15. Development of the Velocity Profile

  16. Development of the Concentration Profile

  17. Results • Simulation trends are comparable to experimental results • Concentration Depletion Near Heat Source • -42% (simulated) • -27% (actual) • Quantitative solution is work in progress

  18. Research Applications • Applied Genetics • Microfluidic Manipulation Technology • Isotope Separation • Thermal diffusion used to separate U235 from U238 • Thermal diffusion responsible for the formation of DNA’s molecular ancestors 3.5 billion years ago?

  19. Acknowledgements • Project Supervisor • Bruce A. Finlayson • Article Authors • Dieter Braun • Albert Libchaber

  20. FEMLAB’s Convection and Conduction equation Convection and Diffusion equation Incompressible Navier-Stokes equation Additional Information (1)Transport equations in terms of non-dimensional numbers

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