335 research outputs found
Semi-analytical solution of multilayer diffusion problems with time-varying boundary conditions and general interface conditions
We develop a new semi-analytical method for solving multilayer diffusion
problems with time-varying external boundary conditions and general internal
boundary conditions at the interfaces between adjacent layers. The convergence
rate of the semi-analytical method, relative to the number of eigenvalues, is
investigated and the effect of varying the interface conditions on the solution
behaviour is explored. Numerical experiments demonstrate that solutions can be
computed using the new semi-analytical method that are more accurate and more
efficient than the unified transform method of Sheils [Appl. Math. Model.,
46:450-464, 2017]. Furthermore, unlike classical analytical solutions and the
unified transform method, only the new semi-analytical method is able to
correctly treat problems with both time-varying external boundary conditions
and a large number of layers. The paper is concluded by replicating solutions
to several important industrial, environmental and biological applications
previously reported in the literature, demonstrating the wide applicability of
the work.Comment: 24 pages, 8 figures, accepted version of paper published in Applied
Mathematics and Computatio
Fast computation of effective diffusivities using a semi-analytical solution of the homogenization boundary value problem for block locally-isotropic heterogeneous media
Direct numerical simulation of diffusion through heterogeneous media can be
difficult due to the computational cost of resolving fine-scale
heterogeneities. One method to overcome this difficulty is to homogenize the
model by replacing the spatially-varying fine-scale diffusivity with an
effective diffusivity calculated from the solution of an appropriate boundary
value problem. In this paper, we present a new semi-analytical method for
solving this boundary value problem and computing the effective diffusivity for
pixellated, locally-isotropic, heterogeneous media. We compare our new solution
method to a standard finite volume method and show that equivalent accuracy can
be achieved in less computational time for several standard test cases. We also
demonstrate how the new solution method can be applied to complex heterogeneous
geometries represented by a grid of blocks. These results indicate that our new
semi-analytical method has the potential to significantly speed up simulations
of diffusion in heterogeneous media.Comment: 29 pages, 4 figures, 5 table
Numerical investigation into coarse-scale models of diffusion in complex heterogeneous media
Computational modelling of diffusion in heterogeneous media is prohibitively
expensive for problems with fine-scale heterogeneities. A common strategy for
resolving this issue is to decompose the domain into a number of
non-overlapping sub-domains and homogenize the spatially-dependent diffusivity
within each sub-domain (homogenization cell). This process yields a
coarse-scale model for approximating the solution behaviour of the original
fine-scale model at a reduced computational cost. In this paper, we study
coarse-scale diffusion models in block heterogeneous media and investigate, for
the first time, the effect that various factors have on the accuracy of
resulting coarse-scale solutions. We present new findings on the error
associated with homogenization as well as recommendations for choosing the
number of homogenization cells and the type of boundary condition imposed on
the homogenization cells to produce accurate coarse-scale solutions.Comment: 19 pages, 10 figures, submitte
BISON: bio-interface for the semi-global analysis of network patterns
BACKGROUND: The large amount of genomics data that have accumulated over the past decade require extensive data mining. However, the global nature of data mining, which includes pattern mining, poses difficulties for users who want to study specific questions in a more local environment. This creates a need for techniques that allow a localized analysis of globally determined patterns. RESULTS: We developed a tool that determines and evaluates global patterns based on protein property and network information, while providing all the benefits of a perspective that is targeted at biologist users with specific goals and interests. Our tool uses our own data mining techniques, integrated into current visualization and navigation techniques. The functionality of the tool is discussed in the context of the transcriptional network of regulation in the enteric bacterium Escherichia coli. Two biological questions were asked: (i) Which functional categories of proteins (identified by hidden Markov models) are regulated by a regulator with a specific domain? (ii) Which regulators are involved in the regulation of proteins that contain a common hidden Markov model? Using these examples, we explain the gene-centered and pattern-centered analysis that the tool permits. CONCLUSION: In summary, we have a tool that can be used for a wide variety of applications in biology, medicine, or agriculture. The pattern mining engine is global in the way that patterns are determined across the entire network. The tool still permits a localized analysis for users who want to analyze a subportion of the total network. We have named the tool BISON (Bio-Interface for the Semi-global analysis Of Network patterns)
Bose-Einstein condensates in standing waves: The cubic nonlinear Schroedinger equation with a periodic potential
We present a new family of stationary solutions to the cubic nonlinear
Schroedinger equation with a Jacobian elliptic function potential. In the limit
of a sinusoidal potential our solutions model a dilute gas Bose-Einstein
condensate trapped in a standing light wave. Provided the ratio of the height
of the variations of the condensate to its DC offset is small enough, both
trivial phase and nontrivial phase solutions are shown to be stable. Numerical
simulations suggest such stationary states are experimentally observable.Comment: 4 pages, 4 figure
Augmented Reality Technician Assistance Program
The Augmented Reality Technician Assistance Program is a proof-of-concept project for allowing a remote expert to communicate with and assist a field technician in completing procedures with which the technician may be unfamiliar. For example, an expert in Navy aircraft maintenance could advise an Air Force flight mechanic about performing repairs or maintenance on Navy aircraft. The end goal of our Cedarville computer science capstone project is to create an experimental prototype to deliver to the Air Force Research Laboratory. In our prototype the expert uses a Microsoft Surface Pro tablet to communicate via marked up still images with a Hololens-enabled field technician. As a wearable computer, the Hololens provides the technician a hands-free advantage over traditional devices, because it’s interface does not use typical input devices such as a mouse and keyboard. The advantage of the Surface Pro is that it allows the expert to mark up instructional images naturally with the stylus, providing better precision for the annotations
Pleiotropic phenotypes of a Yersinia enterocolitica flhD mutant include reduced lethality in a chicken embryo model
<p>Abstract</p> <p>Background</p> <p>The <it>Yersinia enterocolitica </it>flagellar master regulator FlhD/FlhC affects the expression levels of non-flagellar genes, including 21 genes that are involved in central metabolism. The sigma factor of the flagellar system, FliA, has a negative effect on the expression levels of seven plasmid-encoded virulence genes in addition to its positive effect on the expression levels of eight of the flagellar operons. This study investigates the phenotypes of <it>flhD </it>and <it>fliA </it>mutants that result from the complex gene regulation.</p> <p>Results</p> <p>Phenotypes relating to central metabolism were investigated with Phenotype MicroArrays. Compared to the wild-type strain, isogenic <it>flhD </it>and <it>fliA </it>mutants exhibited increased growth on purines and reduced growth on N-acetyl-D-glucosamine and D-mannose, when used as a sole carbon source. Both mutants grew more poorly on pyrimidines and L-histidine as sole nitrogen source. Several intermediates of the tricarboxylic acid and the urea cycle, as well as several dipeptides, provided differential growth conditions for the two mutants. Gene expression was determined for selected genes and correlated with the observed phenotypes. Phenotypes relating to virulence were determined with the chicken embryo lethality assay. The assay that was previously established for <it>Escherichia coli </it>strains was modified for <it>Y. enterocolitica</it>. The <it>flhD </it>mutant caused reduced chicken embryo lethality when compared to wild-type bacteria. In contrast, the <it>fliA </it>mutant caused wild-type lethality. This indicates that the virulence phenotype of the <it>flhD </it>mutant might be due to genes that are regulated by FlhD/FlhC but not FliA, such as those that encode the flagellar type III secretion system.</p> <p>Conclusion</p> <p>Phenotypes of <it>flhD </it>and <it>fliA </it>mutants are related to central metabolism and virulence and correlate with gene regulation.</p
Fabrication of low-cost, large-area prototype Si(Li) detectors for the GAPS experiment
A Si(Li) detector fabrication procedure has been developed with the aim of
satisfying the unique requirements of the GAPS (General Antiparticle
Spectrometer) experiment. Si(Li) detectors are particularly well-suited to the
GAPS detection scheme, in which several planes of detectors act as the target
to slow and capture an incoming antiparticle into an exotic atom, as well as
the spectrometer and tracker to measure the resulting decay X-rays and
annihilation products. These detectors must provide the absorption depth,
energy resolution, tracking efficiency, and active area necessary for this
technique, all within the significant temperature, power, and cost constraints
of an Antarctic long-duration balloon flight. We report here on the fabrication
and performance of prototype 2"-diameter, 1-1.25 mm-thick, single-strip Si(Li)
detectors that provide the necessary X-ray energy resolution of 4 keV for
a cost per unit area that is far below that of previously-acquired commercial
detectors. This fabrication procedure is currently being optimized for the
4"-diameter, 2.5 mm-thick, multi-strip geometry that will be used for the GAPS
flight detectors.Comment: Accepted for publication at Nuclear Instrumentation and Methods A, 12
pages, 11 figure
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