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

Jaeseol Cho, Kevin D. Dorfman

Research output: Contribution to journalArticlepeer-review

17 Scopus citations


We use Brownian dynamics simulations to analyze the electrophoretic separation of λ-DNA (48.5 kbp) and T4-DNA (169 kbp) in a hexagonal array of 1μm diameter posts with a 3μm 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 (1 mm) that produces meaningful results for the average electrophoretic mobility and effective diffusion (dispersion) coefficient of these macromolecules as they move through the array. While the simulated electrophoretic mobility for λ-DNA is close to the experimental data, the simulation underestimates the magnitude of the corresponding dispersion coefficient. The simulations predict baseline resolution in a 15 mm device after 7 min using an electric field around 30 V/cm, with the resolution increasing exponentially as the electric field further decreases. The mobility and dispersivity data point out two essential phenomena that have been overlooked in previous models of DNA electrophoresis in post arrays: the relaxation time between collisions and simultaneous collisions with multiple posts.

Original languageEnglish (US)
Pages (from-to)5522-5528
Number of pages7
JournalJournal of Chromatography A
Issue number34
StatePublished - Aug 2010

Bibliographical note

Funding Information:
This work was supported by the David and Lucile Packard Foundation, NSF grant CBET- 0642794 and the Camille and Henry Dreyfus Foundation.


  • Computational modeling
  • DNA electrophoresis
  • Lab on a chip
  • Simulation


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