Permeability calculations in three-dimensional isotropic and oriented fiber networks.

Hydraulic permeabilities of fiber networks are of interest for many applications and have been studied extensively. There is little work, however, on permeability calculations in three-dimensional random networks. Computational power is now sufficient to calculate permeabilities directly by constructing artificial fiber networks and simulating flow through them. Even with today's high-performance computers, however, such an approach would be infeasible for large simulations. It is therefore necessary to develop a correlation based on fiber volume fraction, radius, and orientation, preferably by incorporating previous studies on isotropic or structured networks. In this work, the direct calculations were performed, using the finite element method, on networks with varying degrees of orientation, and combinations of results for flows parallel and perpendicular to a single fiber or an array thereof, using a volume-averaging theory, were compared to the detailed analysis. The detailed model agreed well with existing analytical solutions for square arrays of fibers up to fiber volume fractions of 46% for parallel flow and 33% for transverse flow. Permeability calculations were then performed for isotropic and oriented fiber networks within the fiber volume fraction range of 0.3%-15%. When drag coefficients for spatially periodic arrays were used, the results of the volume-averaging method agreed well with the direct finite element calculations. On the contrary, the use of drag coefficients for isolated fibers overpredicted the permeability for the volume fraction range that was employed. We concluded that a weighted combination of drag coefficients for spatially periodic arrays of fibers could be used as a good approximation for fiber networks, which further implies that the effect of the fiber volume fraction and orientation on the permeability of fiber networks are more important than the effect of local network structure.

Developing quantitative, multiscale models for microgravity crystal growth.

Crystal growth conducted under microgravity conditions has had a profound impact on improving our understanding of melt crystal growth processes. Here, we present a brief history of microgravity crystal growth and discuss the development of appropriate models to interpret and optimize these growth experiments. The need for increased model realism and predictive capability demands new approaches for describing phenomena important at several disparate length scales. Of special importance is the ability to represent three-dimensional and transient continuum transport (flows, heat, and mass transfer), phase-change phenomena (thermodynamics and kinetics), and system design (such as furnace heat transfer during melt growth). An overview of mathematical models and numerical algorithms employed to represent such multiscale effects is presented.

Mass transfer limitations at crystallizing interfaces in an atomic force microscopy fluid cell: a finite element analysis.

Although atomic force microscopy (AFM) has emerged as the preeminent experimental tool for real-time in situ measurements of crystal growth processes in solution, relatively little is known about the mass transfer limitations that may impact these measurements. We present a continuum analysis of flow and mass transfer in an atomic force microscope fluid cell during crystal growth, using data acquired from calcium oxalate monohydrate (COM) crystal growth measurements as a comparison. Steady-state flows and solute concentration fields are computed using a three-dimensional, finite element method implemented on a parallel supercomputer. Steady-state flow results are compared with flow visualization experiments to validate the model. Computations of the flow field demonstrate how nonlinear momentum transport alters the spatial structure of the flow with increasing flow volume, altering mass transport conditions near the AFM cantilever and tip. The simulations demonstrate that the combination of solute depletion from crystal growth and mass transfer resistance lowers the solute concentration in the region between the tip and the crystal compared with the solute concentration at the inlet of the AFM cell. For example, using experimentally measured growth rates for COM, the solute concentration in this region is 3.1% lower than the inlet value because the solute consumed by crystal growth beneath the AFM tip cannot be replenished fully due to mass transport limitations. The simulations also reveal that increasing the flow rate through the cell does not affect this difference significantly because of the inherent shielding by the AFM tip in proximity with the crystal surface. Models such as the one presented here, used in conjunction with AFM measurements, promise more precise interpretations of measurement data.

A diffusion-reaction model for DNA microarray assays.

DNA microarrays are extensively used for the quantification of the degree of differential mRNA expression. The assay involves hybridization of mobile DNA strands with immobilized complementary DNA strands to form duplexes. The overall duplex formation rate depends on the rate of transport of strands in solution to the corresponding spot on the surface, and the rate of the hybridization reaction. We present a theoretical model that incorporates both kinetics of the reversible hybridization reaction and diffusional transport of the labeled strands, and analyze DNA microarray hybridization using this model. Simulations are carried out in a geometrically realistic domain for labeled DNA concentrations corresponding to rare and abundant transcripts for typical assay conditions. The rate of strand diffusion in solution is shown to strongly affect the overall hybridization rate. We compute the minimum inter-spot spacing for replicate spots to enhance sensitivity. We also determine the hybridization time for which reliable estimates of the relative mRNA abundance of two species can be obtained using total fluorescence intensities. An analytical solution for the concentration distribution of mobile strands at intermediate hybridization times provides a convenient tool to calculate the mobile strand concentration profiles. This model provides a framework for the process analysis of all microarray assays currently used for genomic transcriptional analysis.