An Immersed Boundary Method for Flowing DNA through Microfluidic Devices

We have developed an immersed boundary method that allows fast calculation of Brownian dynamics of polymer chains and other particles in complex geometries with fluctuating hydrodynamics. This method is based on general geometry Ewald method which solves the Stokes's equation with distributed regularized point forces with O(N) operations. The implementation is verified against Hasimoto's solution of point force in periodic boundary domain and exact solution for the problem of uniform flow around a solid sphere. Fluctuating hydrodynamics is introduced into the calculation using a midpoint algorithm and Chebyshev polynomial approximation which are both proposed by Fixman. This approach is applied to the flow-driven actuation of a tethered λ-DNA molecule which functions as a soft nanomechanical switching element for microfluidic devices. Comparisons with previous results of electrostatic-driven actuation case has been made.