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.

Realistic Brownian Dynamics simulations of biological molecule separation in nanofluidic devices

“…In other words, for an efficient model, some degree of coarse-graining is required. In this study we show that for the short molecules studied here, our Brownian Dynamics (BD) formulation strikes a good balance between fidelity-e.g., agreement with experimental data-and computational efficiency [compared to more expensive coarse-grained techniques such as Dissipative Particle Dynamics (Duong-Hong et al 2008)]. …”

Dissipative particle dynamics simulation of field-dependent DNA mobility in nanoslits

“…We employed a simple method to effectively simulate the local EOF generated by the counterions around the DNA molecules (Duong-Hong et al 2008b). The electrostatic interactions and the resulting fluid shearing mainly occur within the Debye layer in DNA electrophoresis.…”

“…This model was proven to work well for DNA electrophoresis without creating any fluid motion in the surrounding area(Duong-Hong et al 2008b). They included the approximation of the complex solvent-DNA interactions in the simulation and obtained unperturbed velocity profile of local EOF.…”

Dissipative particle dynamics simulations for fibre suspensions in newtonian and viscoelastic fluids

“…The most advantage of DPD is the easy model of complex fluids at a reasonable computational cost. Some significant successes have been achieved so far with the DPD method, e.g., in suspensions [18][19][20], micro-and nano-fluidic [21,22], and especially with diluted polymer solutions [23][24][25]. Some models of rodlike particles have been introduced by Martys and Mountain [26] and Yamamoto and Matsuoka [27,28].…”