Detailed modeling of entropic trapping and separation of long DNA molecules in nanofilter array devices is required in order to determine the impact of subtle changes in device structure on the overall separation performance. In this paper, we further developed and applied the previously reported dissipative particle dynamics (DPD) simulation, which considers both DNA electrophoresis and electroosmotic flows in patterned nano-filters, in order to determine the impact of a subtle device structural modification. To simulate the free draining mobility, fluid particles within the Debye length of DNA were assumed to carry a positive charge equal to the value of the DNA bead charge, which realistically mimic hydrodynamic conditions near the DNA backbone. Our simulation algorithm was tested rigorously and was validated against several experimental findings. Simulation results showed that the free-draining mobility of DNA can be captured without including computationally expensive electrostatic interactions within Debye layer. Based on the worm-like chain DNA model, we applied our DPD algorithm to two nano-fluidic filters of different geometries. The nominal mobility of DNA chains was found to increase with their length, which is consistent with experimental observations. Apart from the general opinion that a longer DNA chain has higher chance to enter the shallow channel, our studies suggested an additional mechanism for the observed length-dependency of DNA mobility. If the coiled length of a short DNA chain is much smaller than half depth of the trap, it is easily hindered in one corner of the trap where the electric field is rather low, which traps the DNA for a longer time. Our studies also showed that the nominal mobility of DNA chains depends on the geometry of the filter. In the two geometries studied, the shallow channel in the center of the trap more efficiently separate long DNA chains. In different geometries, DNA chains experience different folding ratio when it is hindered in the trap, which might lead to different separation rate. Our studies suggested that the recently realized vertical nanochannel membrane systems should exhibit higher DNA selectivity, compared with the previous, planar nanochannel systems.

Keywords Dissipative particle dynamics (DPD) method, electroosmotic flows, DNA electrophoresis, nano-fluidic filter, DNA separation.