Modeling the Electrophoretic Separation of Short Biological Molecules in Nanofluidic Devices

Fayad, Ghassan N.; Hadjiconstantinou, Nicolas G.

doi:10.1115/1.4023445

Cited by 3 publications

(3 citation statements)

References 19 publications

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“…According to their findings, long rigid DNA branches elute faster in strong electric fields. Fayad and Hadjiconstantinou did similar work, but they studied the effects of different geometrics on entropic trap arrays [108]. Fayad and Hadjiconstantinou used BD simulation with WLC model considering HI to study the effect of device geometry on the separation process for shorter DNAs.…”

Section: Structured Microchannel Arrays For Entropic Trapmentioning

confidence: 99%

Computational Studies of DNA Separations in Micro-Fabricated Devices: Review of General Approaches and Recent Applications

Monjezi¹,

Behdani²,

Palaniappan³

et al. 2017

ACES

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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.

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Section: Structured Microchannel Arrays For Entropic Trapmentioning

confidence: 99%

Computational Studies of DNA Separations in Micro-Fabricated Devices: Review of General Approaches and Recent Applications

Monjezi¹,

Behdani²,

Palaniappan³

et al. 2017

ACES

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“…16 These patterned nanofilter arrays have also been considered ideal experimental platforms to quantitatively understand the hindered molecular transport in porous systems. Many analytical and numerical studies have been performed on such systems for various sieving mechanisms, 10,[17][18][19][20][21][22][23][24][25] however, most theoretical studies have focused on molecular sieving in 1D nanofilter arrays and purely steric interactions. A theoretical attempt at molecular sieving in a 2D nanofilter array was briefly conducted using a steric interaction-based kinetic model derived from a 1D system, but the study did not provide a comprehensive understanding of the 2D nanofilter array.…”

Section: Introductionmentioning

confidence: 99%

Continuous-flow macromolecular sieving in slanted nanofilter array: stochastic model and coupling effect of electrostatic and steric hindrance

Ko,

Park,

Han

2023

Lab Chip

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“…In their program, DNA was modeled as a chain of rigid segments connected by bending, torsion, and stretching potentials, and the Rotne-Prager tensor is used to model hydrodynamic interactions . This model was further adapted by others to study the dynamical behavior of DNA. ,− Recently, the scalable BD package BD_BOX was developed by Trylska and co-authors for the multiscale simulation of systems comprised of various interacting macromolecules using flexible, coarse-grained bead models, where the package has been parallelized using MPI (message passing interface) and OpenMP (open multiprocessing) libraries to speed up the BD simulation of multicomponent systems. − Also, Marenduzzo and co-authors recently developed a coarse-grained BD model for twistable elastic polymers using continuum rod theory based on a previous work of Chirico et al., and the model was implemented in the highly scalable multipurpose MD software package LAMMPS . Most of these BD models were not developed for the simulation of the overdamped conformational dynamics of highly structured DNA assemblies such as scaffolded DNA origami.…”

Section: Introductionmentioning

confidence: 99%

Computing Nonequilibrium Conformational Dynamics of Structured Nucleic Acid Assemblies

Sedeh¹,

Pan²,

Adendorff³

et al. 2015

J. Chem. Theory Comput.

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Synthetic nucleic acids can be programmed to form precise three-dimensional structures on the nanometer-scale. These thermodynamically stable complexes can serve as structural scaffolds to spatially organize functional molecules including multiple enzymes, chromophores, and force-sensing elements with internal dynamics that include substrate reaction-diffusion, excitonic energy transfer, and force-displacement response that often depend critically on both the local and global conformational dynamics of the nucleic acid assembly. However, high molecular weight assemblies exhibit long time-scale and large length-scale motions that cannot easily be sampled using all-atom computational procedures such as molecular dynamics. As an alternative, here we present a computational framework to compute the overdamped conformational dynamics of structured nucleic acid assemblies and apply it to a DNA-based tweezer, a nine-layer DNA origami ring, and a pointer-shaped DNA origami object, which consist of 204, 3,600, and over 7,000 basepairs, respectively. The framework employs a mechanical finite element model for the DNA nanostructure combined with an implicit solvent model to either simulate the Brownian dynamics of the assembly or alternatively compute its Brownian modes. Computational results are compared with an all-atom molecular dynamics simulation of the DNA-based tweezer. Several hundred microseconds of Brownian dynamics are simulated for the nine-layer ring origami object to reveal its long time-scale conformational dynamics, and the first ten Brownian modes of the pointer-shaped structure are predicted.

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Modeling the Electrophoretic Separation of Short Biological Molecules in Nanofluidic Devices

Cited by 3 publications

References 19 publications

Computational Studies of DNA Separations in Micro-Fabricated Devices: Review of General Approaches and Recent Applications

Computational Studies of DNA Separations in Micro-Fabricated Devices: Review of General Approaches and Recent Applications

Continuous-flow macromolecular sieving in slanted nanofilter array: stochastic model and coupling effect of electrostatic and steric hindrance

Computing Nonequilibrium Conformational Dynamics of Structured Nucleic Acid Assemblies

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