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Realistic simulations of combined DNA electrophoretic flow and EOF in nano‐fluidic devices
Author(s) -
DuongHong Duc,
Han Jongyoon,
Wang JianSheng,
Hadjiconstantinou Nicolas G.,
Chen Yu Zong,
Liu GuiRong
Publication year - 2008
Publication title -
electrophoresis
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.666
H-Index - 158
eISSN - 1522-2683
pISSN - 0173-0835
DOI - 10.1002/elps.200800257
Subject(s) - dissipative particle dynamics , electrophoresis , microfluidics , tapering , molecular dynamics , flow (mathematics) , dna , dissipative system , chemical physics , gel electrophoresis of nucleic acids , materials science , mesoscale meteorology , fluidics , trapping , particle (ecology) , nanotechnology , mechanics , chemistry , physics , chromatography , thermodynamics , computer science , computational chemistry , polymer , engineering , composite material , computer graphics (images) , aerospace engineering , ecology , biology , biochemistry , meteorology , oceanography , geology
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 (∼μm) 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.