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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

Trapping of DNA by Thermophoretic Depletion and Convection in FEMLAB

Pawel Drapala

University of Washington

background
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)
experimental setup
Experimental Setup

Infrared Laser

Plasmid size DNA solution suspended in plastic container

slide4

Experimental Results

13 mW

50 μm

400 μm

experimental results
Experimental Results

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

theory
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)
governing equations
Governing Equations
  • Incompressible Navier-Stokes Equation
  • The Energy Equation
  • The Diffusivity Equation
non dimensional numbers
Non-dimensional Numbers
  • Grashoff number
  • Prandtl number
  • Schmidt number
  • Soret number
  • Power number
model geometry2
Model Geometry

Axi-Symmetric Boundary Condition

Insulation and No Slip Boundary Condition

mesh statistics
Mesh Statistics

Number of Degrees of Freedom: 17487

Number of Elements: 2008

Number of Boundary Elements: 68

results
Results
  • Simulation trends are comparable to experimental results
  • Concentration Depletion Near Heat Source
    • -42% (simulated)
    • -27% (actual)
  • Quantitative solution is work in progress
research applications
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?
acknowledgements
Acknowledgements
  • Project Supervisor
    • Bruce A. Finlayson
  • Article Authors
    • Dieter Braun
    • Albert Libchaber
additional information 1 transport equations in terms of non dimensional numbers
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