TITLE:
Computational Studies of DNA Separations in Micro-Fabricated Devices: Review of General Approaches and Recent Applications
AUTHORS:
Saman Monjezi, Behrouz Behdani, Meyyammai B. Palaniappan, James D. Jones, Joontaek Park
KEYWORDS:
DNA Separation, Single Polymer Dynamics, Brownian Dynamics Simulation, Microfluidics, Electrophoresis, Entropic Trap, Microchannel
JOURNAL NAME:
Advances in Chemical Engineering and Science,
Vol.7 No.4,
August
31,
2017
ABSTRACT: DNA separation techniques have drawn attention because of their uses in applications
such as gene analysis and manipulation. There have been many studies
utilizing micro-fabricated devices for faster and more efficient separations
than traditional methods using gel electrophoresis. Although many experimental
studies have presented various new devices and methods, computational
studies have played a pivotal role in this development by identifying
separation mechanisms and by finding optimal designs for efficient separation
conditions. The simulation of DNA separation methods in micro-fabricated
devices requires the correct capture of the dynamics and the structure of a
single polymer molecule that is being affected by an applied flow field or an
electric field in complex geometries. In this work, we summarize the polymer
models (the bead-spring model, the bead-rod model, the slender-body model,
and the touching-bead model) and the methods, focusing on Brownian dynamics
simulation, used to calculate inhomogeneous fields taking into consideration
complex boundaries (the finite element method, the boundary element
method, the lattice-Boltzmann method, and the dissipative particle dynamics
simulation). The worm-like chain model (adapted from the bead-spring
model) combined with the finite element method has been most commonly
used but other models have shown more efficient and accurate results. We also
review the applications of these simulation approaches in various separation
methods and devices: gel electrophoresis, post arrays, capillary electrophoresis,
microchannel flows, entropic traps, nanopores, and rotational flows.
As more complicated geometries are involved in new devices, more rigorous
models (such as incorporating the hydrodynamic interactions of DNA with
solid boundaries) that can correctly capture the dynamic behaviors of DNA in
such devices are needed.