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Title: Particle Interactions in DNA-laden Flows

Abstract

Microfluidic devices are becoming state-of-the-art in many significant applications including pathogen detection, continuous monitoring, and drug delivery. Numerical algorithms which can simulate flows of complex fluids within these devices are needed for their development and optimization. A method is being developed at LLNL by Trebotich et. al. [30] for simulations of DNA-laden flows in complex microscale geometries such as packed bed reactors and pillar chips. In this method an incompressible Newtonian fluid is discretized with Cartesian grid embedded boundary methods, and the DNA is represented by a bead-rod polymer model. The fluid and polymer are coupled through a body force. In its current state, polymer-surface interactions are treated as elastic collisions between beads and surface, and polymer-polymer interactions are neglected. Implementation of polymer-polymer interactions is the main objective of this work. It is achieved by two methods: (1) a rigid constraint whereby rods elastically bounce off one another, and (2) a smooth potential acting between rods. In addition, a smooth potential is also implemented for the polymer-surface interactions. Background information will also be presented as well as related work by other researchers.

Authors:
; ;
Publication Date:
Research Org.:
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
898439
Report Number(s):
UCRL-TR-217843
TRN: US0701909
DOE Contract Number:
W-7405-ENG-48
Resource Type:
Technical Report
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS; 99 GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE; ALGORITHMS; DETECTION; DNA; IMPLEMENTATION; LAWRENCE LIVERMORE NATIONAL LABORATORY; MONITORING; OPTIMIZATION; PACKED BEDS; PARTICLE INTERACTIONS; PATHOGENS; POLYMERS

Citation Formats

Bybee, M D, Miller, G H, and Trebotich, D. Particle Interactions in DNA-laden Flows. United States: N. p., 2005. Web. doi:10.2172/898439.
Bybee, M D, Miller, G H, & Trebotich, D. Particle Interactions in DNA-laden Flows. United States. doi:10.2172/898439.
Bybee, M D, Miller, G H, and Trebotich, D. Tue . "Particle Interactions in DNA-laden Flows". United States. doi:10.2172/898439. https://www.osti.gov/servlets/purl/898439.
@article{osti_898439,
title = {Particle Interactions in DNA-laden Flows},
author = {Bybee, M D and Miller, G H and Trebotich, D},
abstractNote = {Microfluidic devices are becoming state-of-the-art in many significant applications including pathogen detection, continuous monitoring, and drug delivery. Numerical algorithms which can simulate flows of complex fluids within these devices are needed for their development and optimization. A method is being developed at LLNL by Trebotich et. al. [30] for simulations of DNA-laden flows in complex microscale geometries such as packed bed reactors and pillar chips. In this method an incompressible Newtonian fluid is discretized with Cartesian grid embedded boundary methods, and the DNA is represented by a bead-rod polymer model. The fluid and polymer are coupled through a body force. In its current state, polymer-surface interactions are treated as elastic collisions between beads and surface, and polymer-polymer interactions are neglected. Implementation of polymer-polymer interactions is the main objective of this work. It is achieved by two methods: (1) a rigid constraint whereby rods elastically bounce off one another, and (2) a smooth potential acting between rods. In addition, a smooth potential is also implemented for the polymer-surface interactions. Background information will also be presented as well as related work by other researchers.},
doi = {10.2172/898439},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Tue Dec 20 00:00:00 EST 2005},
month = {Tue Dec 20 00:00:00 EST 2005}
}

Technical Report:

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  • 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 rodsmore » and surfaces.« less
  • 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 Coulombicmore » 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.« less
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  • The successful prediction of particle-laden, turbulent flows relies heavily on the representation of turbulence in the gas phase. Several types of turbulence models for single-phase gas flow have been developed which compare reasonably well with experimental data. In the present work, a low-Reynolds'' k-[epsilon], closure model is chosen to describe the Reynolds stresses associated with gas-phase turbulence. This closure scheme, which involves transport equations for the turbulent kinetic energy and its dissipation rate, is valid in the turbulent core as well as the viscous sublayer. Several versions of the low-Reynolds k-[epsilon] closure are documented in the literature. However, even thosemore » models which are similar in theory often differ considerably in their quantitative and qualitative predictions, making the selection of such a model a difficult task. The purpose of this progress report is to document our findings on the performance of ten different versions of the low-Reynolds k-[epsilon] model on predicting fully developed pipe flow. The predictions are compared with the experimental data of Schildknecht, et al. (1979). With the exception of the model put forth by Hoffman (1975), the predictions of all the closures show reasonable agreement for the mean velocity profile. However, important quantitative differences exist for the turbulent kinetic energy profile. In addition, the predicted eddy viscosity profile and the wall-region profile of the turbulent kinetic energy dissipation rate exhibit both quantitative and qualitative differences. An effort to extend the present comparisons to include experimental measurements of other researchers is recommended in order to further evaluate the performance of the models.« less
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