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

PDF Version Also Available for Download.

Description

We present a hybrid fluid-particle algorithm to simulate flow and transport of DNA-laden fluids in microdevices. Relevant length scales in microfluidic systems range from characteristic channel sizes of millimeters to micron scale geometric variation (e.g., post arrays) to 10 nanometers for the length of a single rod in a bead-rod polymer representation of a biological material such as DNA. The method is based on a previous fluid-particle algorithm in which long molecules are represented as a chain of connected rods, but in which the physically unrealistic behavior of rod crossing occurred. We have extended this algorithm to include screened Coulombic ... continued below

Physical Description

PDF-file: 19 pages; size: 0.3 Mbytes

Creation Information

Trebotich, D; Miller, G H & Bybee, M D October 6, 2006.

Context

This article is part of the collection entitled: Office of Scientific & Technical Information Technical Reports and was provided by UNT Libraries Government Documents Department to Digital Library, a digital repository hosted by the UNT Libraries. More information about this article can be viewed below.

Who

People and organizations associated with either the creation of this article or its content.

Publisher

Provided By

UNT Libraries Government Documents Department

Serving as both a federal and a state depository library, the UNT Libraries Government Documents Department maintains millions of items in a variety of formats. The department is a member of the FDLP Content Partnerships Program and an Affiliated Archive of the National Archives.

Contact Us

What

Descriptive information to help identify this article. Follow the links below to find similar items on the Digital Library.

Description

We present a hybrid fluid-particle algorithm to simulate flow and transport of DNA-laden fluids in microdevices. Relevant length scales in microfluidic systems range from characteristic channel sizes of millimeters to micron scale geometric variation (e.g., post arrays) to 10 nanometers for the length of a single rod in a bead-rod polymer representation of a biological material such as DNA. The method is based on a previous fluid-particle algorithm in which long molecules are represented as a chain of connected rods, but in which the physically unrealistic behavior of rod crossing occurred. We have extended this algorithm to include screened Coulombic forces between particles by implementing a Debye-Hueckel potential acting between rods. In the method an unsteady incompressible Newtonian fluid is discretized with a second-order finite difference method in the interior of the Cartesian grid domain; an embedded boundary volume-of-fluid formulation is used near boundaries. The bead-rod polymer model is fully coupled to the solvent through body forces representing hydrodynamic drag and stochastic thermal fluctuations. While intrapolymer interactions are modeled by a soft potential, polymer-structure interactions are treated as perfectly elastic collisions. We demonstrate this method on flow and transport of a polymer through a post array microchannel in 2D where the polymer incorporates more realistic physical parameters of DNA, and compare to previous simulations where rods are allowed to cross. We also show that the method is capable of simulating 3D flow in a packed bed micro-column.

Physical Description

PDF-file: 19 pages; size: 0.3 Mbytes

Source

  • Journal Name: Journal of Nanoscience and Nanotechnology, vol. 8, no. 7, July 1, 2008, pp. 3749-3756; Journal Volume: 8; Journal Issue: 7

Language

Item Type

Identifier

Unique identifying numbers for this article in the Digital Library or other systems.

  • Report No.: UCRL-JRNL-225206
  • Grant Number: W-7405-ENG-48
  • Office of Scientific & Technical Information Report Number: 940153
  • Archival Resource Key: ark:/67531/metadc896397

Collections

This article is part of the following collection of related materials.

Office of Scientific & Technical Information Technical Reports

Reports, articles and other documents harvested from the Office of Scientific and Technical Information.

Office of Scientific and Technical Information (OSTI) is the Department of Energy (DOE) office that collects, preserves, and disseminates DOE-sponsored research and development (R&D) results that are the outcomes of R&D projects or other funded activities at DOE labs and facilities nationwide and grantees at universities and other institutions.

What responsibilities do I have when using this article?

When

Dates and time periods associated with this article.

Creation Date

  • October 6, 2006

Added to The UNT Digital Library

  • Sept. 27, 2016, 1:39 a.m.

Description Last Updated

  • Nov. 30, 2016, 4:18 p.m.

Usage Statistics

When was this article last used?

Congratulations! It looks like you are the first person to view this item online.

Interact With This Article

Here are some suggestions for what to do next.

Start Reading

PDF Version Also Available for Download.

International Image Interoperability Framework

IIF Logo

We support the IIIF Presentation API

Trebotich, D; Miller, G H & Bybee, M D. A Penalty Method to Model Particle Interactions in DNA-laden Flows, article, October 6, 2006; Livermore, California. (digital.library.unt.edu/ark:/67531/metadc896397/: accessed November 19, 2018), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.