Brownian dynamics simulations of electrophoretic DNA separations in a sparse ordered post array.

We use Brownian dynamics simulations to analyze the electrophoretic separation of lambda-DNA (48.5kbp) and T4-DNA (169kbp) in a hexagonal array of 1microm diameter posts with a 3microm center-to-center distance. The simulation method takes advantage of an efficient interpolation algorithm for the non-uniform electric field to reach an ensemble size (100 molecules) and simulation length scale (1mm) that produces meaningful results for the average electrophoretic mobility and effective diffusion (dispersion) coefficient of these macromolecules as they move through the array.

Electrophoretic collision of a DNA molecule with a small elliptical obstacle.

We present a Brownian dynamics study of the collision and unhooking of a lambda-DNA molecule with an elliptical obstacle. The semi-major and semi-minor axes of the obstacle are comparable to the radius of gyration of the DNA, and the field is sufficiently strong to cause frequent hairpin formation upon collision. We focus on how the dynamics of a head-on collision (impact parameter of zero) are affected by the angle between the major axis of the ellipse and the direction of the electric field far from the elliptical surface.

DNA electrophoresis in a sparse ordered post array.

We present a study of the electrophoresis of long DNA in a strong electric field through a hexagonal array of cylindrical microscale posts spaced such that the pore size is commensurate with equilibrium coil size of the DNA. Experimental mobility, dispersivity, and videomicroscopy data indicate that the DNA frequently collide with the posts, contradicting previous Brownian dynamics studies using a uniform electric field. We demonstrate via simulations that the frequent collisions, which are essential to separations in these devices, are due to the nonuniform electric field, highlighting the importance of accounting for electric-field gradients when modeling DNA transport in microfluidic devices.

DNA unhooking from a single post as a deterministic process: insights from translocation modeling.

Using stochastic methods developed for DNA translocation through nanopores, we study the unhooking of a long DNA chain from an isolated stationary micropost. Such methods quickly and efficiently furnish both the full probability distribution of the unhooking time and the ensuing moments for a wide range of chain and field parameters. The results compare favorably to more realistic but computationally intense Brownian dynamics simulations.

A boundary element method/Brownian dynamics approach for simulating DNA electrophoresis in electrically insulating microfabricated devices.

We present an approach for merging boundary element method (BEM) solutions of the electric field in electrically insulating complex geometries with Brownian dynamics (BD) simulations of DNA electrophoresis therein. Although a rote application of the standard BEM algorithm proves inaccurate and prohibitively expensive, we show that regularization of the near-wall electric field and an updating scheme commensurate with the characteristic length scale of the BD simulation furnishes a robust, efficient simulation protocol. The accuracy of the BEM-BD method is verified by simulating lambda-DNA collisions with an isolated, insulating cylindrical obstacle and comparing the results with equivalent BD simulations that employ the exact solution for the electric field.