A Penalty Method to Model Particle Interactions in DNA-Laden Flows

Trebotich, David; Miller, Gregory H.; Bybee, Michael D.

doi:10.1166/jnn.2008.006

Cited by 23 publications

(18 citation statements)

References 6 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Polyaniline (PANI), with unique electrical and optical properties, is a promising candidate for wide range of potential applications [9,10]. The changes in electrical and optical properties of PANI induced through interaction of oxidizing or reducing agents make it suitable for sensing applications [11][12][13][14][15][16]. However, the processing difficulty and poor stability due to polymer degradation, have to be overcome for its successful applications.…”

Section: Introductionmentioning

confidence: 99%

Spectroscopic, Kinetic Studies of Polyaniline-Flyash Composite

Khan¹,

Khare²,

Baruah³

et al. 2011

ACES

View full text Add to dashboard Cite

Polyaniline-fly ash (PANI-FA) composites were prepared by oxidative polymerization of aniline with fly ash in presence of ammonium persulphate (APS). The PANI-FA composites were prepared with different concentrations of fly ash to aniline ratio. The composites, so prepared, were characterized by UV-vis spectroscopy, Fourier transform infrared (FTIR) spectroscopy, scanning electron microscopy (SEM) and thermogravimetric analysis (TGA). The thermal stability was studied by TGA and total weight loss of PANI, FA and PANI-FA composites having FA composition of 0.02%, 0.1%, 0.5% and 1.0% were found to be 82%, 39%, 67% 65%, 62% and 61%, respectively. The UV-vis spectroscopy of the PANI-FA polymeric composite shows absorption maxima at 315 and 350 nm (due to π-π* transition of the benzenoid rings), and 578-712 nm (due to charge transfer excitations of the quinoid structure), which are characteristic of emeraldine base. FTIR spectra of the PANI-FA composite is similar to that of pure polyaniline (PANI) but with the bands for C = N, C = C and C-N shifted to lower wave numbers, i.e., 1585, 1494, 1327 and 1113 cm −1 due to strong interaction of Fe 2 O 3 and PANI matrix. SEM shows the complexation of metal oxide with emaraldine base of PANI, significantly changing the aggregate state of polymeric molecular chain.

show abstract

Section: Introductionmentioning

confidence: 99%

Spectroscopic, Kinetic Studies of Polyaniline-Flyash Composite

Khan¹,

Khare²,

Baruah³

et al. 2011

ACES

View full text Add to dashboard Cite

show abstract

“…The second order, finite volume, strongly conservative Schwartz, et al algorithm [31] has been used in many larger applications, including incompressible Navier Stokes with moving boundaries [26], compressible Navier Stokes [15] and a DNA-transport application [37]. We compare our algorithm to the Schwartz, et al algorithm by comparing both eigenvalue spectrums and the how many degrees of freedom are required to achieve a given degree of accuracy.…”

Section: Prior Artmentioning

confidence: 99%

A fourth-order Cartesian grid embedded boundary method for Poisson’s equation

Devendran

Graves

Johansen

et al. 2017

Commun. Appl. Math. Comput. Sci.

View full text Add to dashboard Cite

In this paper, we present an fourth order algorithm to solve Poisson's equation in two and three dimensions. We use a Cartesian grid, embedded boundary method to resolve complex boundaries. We use a weighted least squares algorithm to solve for our stencils. We use convergence tests to demonstrate accuracy and we show the eigenvalues of the operator to demonstrate stability. We compare accuracy and performance with an established second order algorithm. We also discuss in depth strategies for retaining higher order accuracy in the presence of non-smooth geometries.

show abstract

“…The restriction to 2D is useful and can be reduced to model a single molecule traveling through a smaller section of the array. This is the model problem where we have honed the algorithm development to model relevant physics of the flow for the full 3D problem [8,9].…”

Section: Background and Motivationmentioning

confidence: 99%

Numerical Simulation of Polymer Flow in Microfluidic Devices

Kallemov¹,

Miller²,

Trebotich³

2010

Proceedings of the 2009 SIAM Conference on “Mathematics for Industry”

View full text Add to dashboard Cite

We present simulation results from a computational model of polymer flow in microfluidic devices. This work is important because computational models are needed to design miniaturized biomedical devices which leverage microfluidics technology for many significant applications including pathogen detection as well as continuous monitoring and drug delivery involving the processing of polymer molecules such as DNA. Currently, advanced algorithms in design tools are non-existent but necessary to understand the complex fluid and polymer dynamics involved in biological flow at small scales. Our model is based on a fully coupled (including reverse coupling from particle to fluid) fluid-particle numerical algorithm with both stochastic and deterministic components in a bead-rod polymer representation. The particle method is strong second-order accurate, as is the CFD solver. The latter provides a high performance computing platform based on adaptive, embedded boundary methods for these computationally intensive problems with multiple scales. We demonstrate our method on the test problem of flow of DNA molecules in a 2D entropic trap, the square well geometry of which is fundamental component in microfluidic processing yet complicated enough to elicit complex flow features relevant to design. Background and MotivationUnderstanding complex biological flows through advanced algorithmic modeling is critical to many biomedical applications of significance in an array of industries such as targeted drug delivery in pharmaceuticals, continuous monitoring and diagnostics in biotechnology, and fuel cells in energy. These applications will leverage state-of-the-art miniaturized technology, development which requires understanding of the fundamental physics and chemistry of biological fluids at much smaller than normal scales to design and optimize trustworthy working devices, and to get them to market more quickly and with less cost.

show abstract

A Penalty Method to Model Particle Interactions in DNA-Laden Flows

Cited by 23 publications

References 6 publications

Spectroscopic, Kinetic Studies of Polyaniline-Flyash Composite

Spectroscopic, Kinetic Studies of Polyaniline-Flyash Composite

A fourth-order Cartesian grid embedded boundary method for Poisson’s equation

Numerical Simulation of Polymer Flow in Microfluidic Devices

Contact Info

Product

Resources

About