A Hard Constraint Algorithm to Model Particle Interactions in DNA-laden Flows

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Description

We present a new method for particle interactions in polymer models of DNA. The DNA is represented by a bead-rod polymer model and is fully-coupled to the fluid. The main objective in this work is to implement short-range forces to properly model polymer-polymer and polymer-surface interactions, specifically, rod-rod and rod-surface uncrossing. Our new method is based on a rigid constraint algorithm whereby rods elastically bounce off one another to prevent crossing, similar to our previous algorithm used to model polymer-surface interactions. We compare this model to a classical (smooth) potential which acts as a repulsive force between rods, and rods ... continued below

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12 p. (0.3 MB)

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Trebotich, D; Miller, G H & Bybee, M D August 1, 2006.

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Description

We present a new method for particle interactions in polymer models of DNA. The DNA is represented by a bead-rod polymer model and is fully-coupled to the fluid. The main objective in this work is to implement short-range forces to properly model polymer-polymer and polymer-surface interactions, specifically, rod-rod and rod-surface uncrossing. Our new method is based on a rigid constraint algorithm whereby rods elastically bounce off one another to prevent crossing, similar to our previous algorithm used to model polymer-surface interactions. We compare this model to a classical (smooth) potential which acts as a repulsive force between rods, and rods and surfaces.

Physical Description

12 p. (0.3 MB)

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PDF-file: 12 pages; size: 0.3 Mbytes

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  • Journal Name: Nanoscale and Microscale Thermophysical Engineering, vol. 11, no. 1, January 1, 2007, pp. 121-128; Journal Volume: 11; Journal Issue: 1

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  • Report No.: UCRL-JRNL-223318
  • Grant Number: W-7405-ENG-48
  • Office of Scientific & Technical Information Report Number: 940141
  • Archival Resource Key: ark:/67531/metadc893574

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Office of Scientific & Technical Information Technical Reports

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

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  • August 1, 2006

Added to The UNT Digital Library

  • Sept. 27, 2016, 1:39 a.m.

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  • April 13, 2017, 4:22 p.m.

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Trebotich, D; Miller, G H & Bybee, M D. A Hard Constraint Algorithm to Model Particle Interactions in DNA-laden Flows, article, August 1, 2006; Livermore, California. (digital.library.unt.edu/ark:/67531/metadc893574/: accessed November 24, 2017), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.