Modeling and high performance simulation of electrophoretic techniques in microfluidic chips

Kler, Pablo A.; Berli, Claudio Luis Alberto; Guarnieri, Fabio Ariel

doi:10.1007/s10404-010-0660-x

Cited by 25 publications

(30 citation statements)

References 49 publications

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“…This simulation tool was already validated for several analytical applications (Kler et al 2011(Kler et al , 2013. The simulations were performed on a desktop computer with single quad-core Intel i7 3770 3.4 GHz processor, 16 GB DDR3-1066 memory, using 4 calculation threads.…”

Section: Softwarementioning

confidence: 99%

A quantitative model for lateral flow assays

Kler

2016

Microfluid Nanofluid

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Section: Softwarementioning

confidence: 99%

A quantitative model for lateral flow assays

Kler

2016

Microfluid Nanofluid

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“…Visualization and post-processing are carried out in Paraview 3.6. Further details are given in Kler et al (2010) an references therein.…”

Section: Numerical Simulationmentioning

confidence: 99%

Laser fabrication of micropores and their integration to microfluidic platforms for DNA electrophoresis

et al. 2012

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The work presents an alternative method for the manufacture of micropores by using the combination of laser ablation and wet etching. The process of laser ablation was done on silicon (Si) wafers with silicon nitride (Si 3 N 4 ) used as a sacrificial layer. The size of the pores was carefully controlled by following an optical technique. The method exhibits a series of advantages in relation micromachining techniques previously used. The fabricated pores were then integrated to polydimethylsiloxane (PDMS) microchannels, which constitutes a novel setup to be considered for microfluidic applications. Furthermore, as the system is addressed to study the electrically-driven transport of macromolecules, deoxyribonucleic acid (DNA) electrophoresis was performed in the fabricated microsystems to prove the principle. Also for these purposes, the electric field throughout the microchannel and pore region was studied in details by using numerical simulations.

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“…Also three-dimensional parallel simulations of electrophoretic separation with continuum approaches have been reported. The finite element simulations in [34] consider the buffer composition and the ζ-potential at channel walls. In [35,36] mixed finite element and finite difference simulations of protein separation were performed on up to 32 processes.…”

Section: Related Workmentioning

confidence: 99%

A scalable multiphysics algorithm for massively parallel direct numerical simulations of electrophoretic motion

Bartuschat¹,

Rüde²

2018

Journal of Computational Science

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In this article we introduce a novel coupled algorithm for massively parallel direct numerical simulations of electrophoresis in microfluidic flows. This multiphysics algorithm employs an Eulerian description of fluid and ions, combined with a Lagrangian representation of moving charged particles. The fixed grid facilitates efficient solvers and the employed lattice Boltzmann method can efficiently handle complex geometries. Validation experiments with more than 70 000 time steps are presented, together with scaling experiments with over 4 · 10 6 particles and 1.96 · 10 11 grid cells for both hydrodynamics and electric potential. We achieve excellent performance and scaling on up to 65 536 cores of a current supercomputer.At the finest level of resolution, fluid, ions, and particles are simulated by Lagrangian approaches. These explicit solvent methods [37] typically apply coarse-grained molecular dynamics (MD) models to describe the motion of fluid molecules and incorporate Brownian motion [38]. The mesoscale dissipative particle dynamics method is applied in [39] to simulate electrophoresis of a polyelectrolyte in a nanochannel. Another explicit solvent method is presented in [40] for simulating DNA electrophoresis, modeling DNA as a polymer. In both methods the polymer is represented by bead-spring chains with beads represented by a truncated Lennard-Jones potential and connected by elastic spring potentials. Explicit solvent models, however, are computationally very expensive, especially for large numbers of fluid molecules due to pairwise interactions [40]. Moreover, the resolution of solvent, macromolecules, and ions on the same scale limits the maximal problem sizes that can be simulated [41]. Also the mapping of measurable properties from colloidal suspensions to these particle-based methods is problematic [37]. The high computational effort is significantly reduced in implicit particle-based methods that incorporate hydrodynamic interactions into the inter-particle forces. Such methods are applied in [37] and [42] to simulate electrophoretic deposition under consideration of Brownian motion and van der Waals forces. Nevertheless, these methods are restricted to few particle shapes and hydrodynamic interactions in Stokes flow.Euler-Lagrange methods constitute the intermediate level of resolution. These approaches employ Eulerian methods to simulate the fluid phase, whereas the motion of individual particles is described by Newtonian mechanics. For simulations of particles in steady-state motion, the resolved particles can be modeled as fixed while the moving fluid is modeled by an Eulerian approach. In [43] the finite volume method is applied to simulate electrophoresis of up to two stagnant toroids in a moving fluid, employing the Hückel approximation for a fixed ζ-potential and different electrical double layer thicknesses. The steady-state electrophoretic motion of particles with low surface potentials under a weak applied electric field in a charged cylindrical pore is simulated in [44] for a single c...

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Modeling and high performance simulation of electrophoretic techniques in microfluidic chips

Cited by 25 publications

References 49 publications

A quantitative model for lateral flow assays

A quantitative model for lateral flow assays

Laser fabrication of micropores and their integration to microfluidic platforms for DNA electrophoresis

A scalable multiphysics algorithm for massively parallel direct numerical simulations of electrophoretic motion

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