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FY05 LDRD Final Report A Computational Design Tool for Microdevices and Components in Pathogen Detection Systems

Description: We have developed new algorithms to model complex biological flows in integrated biodetection microdevice components. The proposed work is important because the design strategy for the next-generation Autonomous Pathogen Detection System at LLNL is the microfluidic-based Biobriefcase, being developed under the Chemical and Biological Countermeasures Program in the Homeland Security Organization. This miniaturization strategy introduces a new flow regime to systems where biological flow is already complex and not well understood. Also, design and fabrication of MEMS devices is time-consuming and costly due to the current trial-and-error approach. Furthermore, existing devices, in general, are not optimized. There are several MEMS CAD capabilities currently available, but their computational fluid dynamics modeling capabilities are rudimentary at best. Therefore, we proposed a collaboration to develop computational tools at LLNL which will (1) provide critical understanding of the fundamental flow physics involved in bioMEMS devices, (2) shorten the design and fabrication process, and thus reduce costs, (3) optimize current prototypes and (4) provide a prediction capability for the design of new, more advanced microfluidic systems. Computational expertise was provided by Comp-CASC and UC Davis-DAS. The simulation work was supported by key experiments for guidance and validation at UC Berkeley-BioE.
Date: February 7, 2006
Creator: Trebotich, D.
Partner: UNT Libraries Government Documents Department

Modeling Complex Biological Flows in Multi-Scale Systems using the APDEC Framework

Description: We have developed advanced numerical algorithms to model biological fluids in multiscale flow environments using the software framework developed under the SciDAC APDEC ISIC. The foundation of our computational effort is an approach for modeling DNA-laden fluids as ''bead-rod'' polymers whose dynamics are fully coupled to an incompressible viscous solvent. The method is capable of modeling short range forces and interactions between particles using soft potentials and rigid constraints. Our methods are based on higher-order finite difference methods in complex geometry with adaptivity, leveraging algorithms and solvers in the APDEC Framework. Our Cartesian grid embedded boundary approach to incompressible viscous flow in irregular geometries has also been interfaced to a fast and accurate level-sets method within the APDEC Framework for extracting surfaces from volume renderings of medical image data and used to simulate cardio-vascular and pulmonary flows in critical anatomies.
Date: June 24, 2006
Creator: Trebotich, D
Partner: UNT Libraries Government Documents Department

Simulation of Flow and Transport at the Micro (Pore) Scale

Description: An important problem in porous media involves the ability of micron and submicron-sized biological particles such as viruses or bacteria to move in groundwater systems through geologic media characterized by rock or mixed gravel, clay and sand materials. Current simulation capabilities require properly upscaled (continuum) models of colloidal filtration and adsorption to augment existing theories of fluid flow and chemical transport. Practical models typically address flow and transport behavior in aquifers over distances of 1 to 10 km where, for example, fluid momentum balance is governed by the simple Darcy's Law as a function of a pressure gradient, elevation gradient and a medium-dependent permeability parameter. In addition to fluid advection, there are multiple transport processes occurring in these systems including diffusion, dispersion and chemical interactions with solids or other aqueous chemical species. Particle transport is typically modeled in the same way as dissolved species, except that additional loss terms are incorporated to model particle filtration (physical interception), adsorption (chemical interception) and inactivation. Proper resolution of these processes at the porous medium continuum scale constitutes an important closure problem in subsurface science. We present a new simulation capability based on enabling technologies developed for microfluidics applications to model transport of colloidal-sized particles at the microscale, with relevance to the pore scale in geophysical subsurface systems. Particulate is represented by a bead-rod polymer model and is fully-coupled to a Newtonian solvent described by Navier-Stokes. Finite differences are used to discretize the interior of the domain; a Cartesian grid embedded boundary/volume-of-fluid method is used near boundaries and interfaces. This approach to complex geometry is amenable to direct simulation on grids obtained from surface extractions of tomographic image data. Short-range interactions are included in the particle model. This capability has been previously demonstrated on polymer flow in spatially-resolved packed bed (3D) and post array ...
Date: April 5, 2007
Creator: Trebotich, D & Miller, G H
Partner: UNT Libraries Government Documents Department

Toward a Mesoscale Model for the Dynamics of Polymer Solutions

Description: To model entire microfluidic systems containing solvated polymers we argue that it is necessary to have a numerical stability constraint governed only by the advective CFL condition. Advancements in the treatment of Kramers bead-rod polymer models are presented to enable tightly-coupled fluid-particle algorithms in the context of system-level modeling.
Date: October 2, 2006
Creator: Miller, G H & Trebotich, D
Partner: UNT Libraries Government Documents Department

Incorporating Electrokinetic Phenomena into EBNavierStokes

Description: Motivated by the recent interest in using electrokinetic effects within microfluidic devices, they have extended the EBNavierStokes code to be able to handle electrokinetic effects. With this added functionality, the code becomes more useful for understanding and designing microfluidic devices that take advantage of electrokinetic effects (e.g. pumping and mixing). Supporting the simulation of electrokinetic effects required three main extensions to the existing code: (1) addition of an electric field solver, (2) development of a module for accurately computing the Smulochowski slip-velocity at fluid-solid boundaries, and (3) extension of the fluid solver to handle nonuniform inhomogeneous Dirichlet boundary conditions. The first and second extensions were needed to compute the electrokinetically generated slip-velocity at fluid-solid boundaries. The third extension made it possible for the fluid flow to be driven by a slip-velocity boundary condition (rather than by a pressure difference between inflow and outflow). In addition, several small changes were made throughout the code to make it compatible with these extensions. This report documents the changes to the EBNavierStokes code required to support the simulation of electrokinetic effects. They begin with a brief overview of the problem of electrokinetically driven flow. Next, they present a detailed description of the changes to the EBNavierStokes code. Finally, they present some preliminary results and discuss future directions and improvements to the code.
Date: January 10, 2006
Creator: Chu, K & Trebotich, D
Partner: UNT Libraries Government Documents Department

Particle Interactions in DNA-laden Flows

Description: 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.
Date: December 20, 2005
Creator: Bybee, M D; Miller, G H & Trebotich, D
Partner: UNT Libraries Government Documents Department

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

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.
Date: August 1, 2006
Creator: Trebotich, D; Miller, G H & Bybee, M D
Partner: UNT Libraries Government Documents Department

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

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.
Date: October 6, 2006
Creator: Trebotich, D; Miller, G H & Bybee, M D
Partner: UNT Libraries Government Documents Department

An investigation of the effect of pore scale flow on average geochemical reaction rates using direct numerical simulation

Description: The scale-dependence of geochemical reaction rates hinders their use in continuum scale models intended for the interpretation and prediction of chemical fate and transport in subsurface environments such as those considered for geologic sequestration of CO{sub 2}. Processes that take place at the pore scale, especially those involving mass transport limitations to reactive surfaces, may contribute to the discrepancy commonly observed between laboratory-determined and continuum-scale or field rates. Here, the dependence of mineral dissolution rates on the pore structure of the porous media is investigated by means of pore scale modeling of flow and multicomponent reactive transport. The pore scale model is comprised of high performance simulation tools and algorithms for incompressible flow and conservative transport combined with a general-purpose multicomponent geochemical reaction code. The model performs direct numerical simulation of reactive transport based on an operator-splitting approach to coupling transport and reactions. The approach is validated with a Poiseuille flow single-pore experiment and verified with an equivalent 1D continuum-scale model of a capillary tube packed with calcite spheres. Using the case of calcite dissolution as an example, the high resolution model is used to demonstrate that non-uniformity in the flow field at the pore scale has the effect of decreasing the overall reactivity of the system, even when systems with identical reactive surface area are considered. The effect becomes more pronounced as the heterogeneity of the reactive grain packing increases, particularly where the flow slows sufficiently such that the solution approaches equilibrium locally and the average rate becomes transport-limited.
Date: February 1, 2012
Creator: Rafa, S. Molins; Trebotich, D.; Steefel, C. I. & Shen, C.
Partner: UNT Libraries Government Documents Department