title: Realistic simulations of combined DNA electrophoretic flow and EOF in nano-fluidic devices.
abstract: We present a three-dimensional dissipative particle dynamics model of DNA electrophoretic flow that captures both DNA stochastic motion and hydrodynamics without requiring expensive molecular dynamics calculations. This model enables us to efficiently and simultaneously simulate DNA electrophoretic flow and local EOF (generated by counterions near the DNA backbone), in mesoscale (~microm) fluidic devices. Our model is used to study the electrophoretic separation of long DNA chains under entropic trapping conditions [Han and Craighead, Science 2000, 288, 1026-1029]. Our simulation results are in good agreement with experimental data for realistic geometries (tapered walls) and reveal that wall tapering in entropic traps has a profound impact in the DNA trapping behavior, an effect which was largely ignored in previous modeling.
authors.affiliation: Abbott Vascular, Santa Clara, CA 95054, USA. duc.duong@av.abbott.com
authors.forename: Duc
authors.initials: D
authors.lastname: Duong-Hong
authors.forename: Jongyoon
authors.initials: J
authors.lastname: Han
authors.forename: Jian-Sheng
authors.initials: JS
authors.lastname: Wang
authors.forename: Nicolas G
authors.initials: NG
authors.lastname: Hadjiconstantinou
authors.forename: Yu Zong
authors.initials: YZ
authors.lastname: Chen
authors.forename: Gui-Rong
authors.initials: GR
authors.lastname: Liu
mesh_terms: D003198:Computer Simulation; D004247:DNA / Q000032:analysis / Q000737:chemistry* / Q000302:isolation & purification; D046209:Electrophoresis, Microchip / Q000295:instrumentation* / Q000379:methods; D046210:Microfluidic Analytical Techniques / Q000295:instrumentation*; D044085:Microfluidics / Q000379:methods; D049329:Nanostructures / Q000737:chemistry*
chemical_list: D004247:DNA