Numerical tidal models with unequal grid-spacing

Thesis (M.S.) University of Alaska Fairbanks, 2006A two-dimensional alternating-direction implicit numerical tidal model with unequal grid-spacing is developed and successfully tested. The method is essentially an extension into two dimensions of a one-dimensional implicit method in which tide heights and flow rates are evaluated on the same cross-sections, an approach which permits a river to be schematized into a number of sections of differing lengths. The two-dimensional scheme gives the user considerable control over the density of the computation points in a region by virtue of the fact that heights and depth-mean currents are evaluated midway between points of intersection of a grid constructed from orthogonal lines, the spacing between which may be chosed at will. The method is applied initially to the Irish Sea using a grid of constant spacing. The effects of increasing time step and friction on stability and accuracy are investigated, and the model is proved to be unconditionally stable. The results match those of previous investigators, and some new information on the M₂ currents of the region is obtained. The second application of the model is to a 'rectangular' North Sea, a favorable comparison being obtained when the region is schematized by two grids of equal and unequal spacing. Finally, the model is applied to Cook Inlet, Alaska, a region of complexity sufficient to warrant the use of a scheme possessing the unequal grid-spacing feature. Satisfactory results are obtained after tuning the model by adjustment of the friction coefficient. Movie films were made in order to conceptually clarify the tidal behaviors of the Irish Sea and Cook Inlet. Each film shows as functions of time, perspective views of the sea surface, and current vectors superimposed on a contour map of the sea surface.I. Introduction -- II. Hydraulic calculations using the harmonic method -- III. Hydraulic calculations using the one-dimensional implicit method -- IV. A two-dimensional model with unequal grid-spacing -- V. The finite-difference equations and their solution -- VI. Programming considerations -- VII. Application of the model to the Irish Sea -- VIII. Application of the model to a rectangular North Sea -- IX. Application of the model to Cook Inlet, Alaska -- X. Additional results of interest -- XI. Conclusions -- References -- Appendix I. The harmonic method : calculation of L,M,N, and O -- Appendix II. Example of branch-point solution for the harmonic method -- Appendix III. Analysis of stability and wave-deformation for the one-dimensional implicit method -- Appendix IV. Compact form of the finite-difference equations for the one-dimensional implicit method -- Appendix V. Example of branch-point solution for the one-dimensional implicit method -- Appendix VI. Compact form of the finite-difference equations for the two-dimensional implicit method

A variable-boundary numerical tidal model

Thesis (M.S.) University of Alaska Fairbanks, 1970A numerical tidal model using equations developed by Hansen (1952) and Yuen (1967) is automated to the point where a potential user need not undertake extensive reprogramming. The user adds to the program only those cards needed to specify tides at input points as a function of time; the application of the relevant calculations at each grid point being controlled by an integer matrix that corresponds to the inlet boundary. A sample problem is covered in detail and applications of the model to the M₂ tide of the Gulf of California, and to a hypothetical mean tide in Cook Inlet are shown.I. Introdution -- II. The calculation of tides in inlets -- III. The finite difference equations -- IV. Automation of the sequence of calculations -- V. Program arrangement -- VI. Grid selection and data arrangement -- VII. Computer outputs and data analysis -- VIII. A sample problem -- IX. Two applictations of the model -- Bibliography -- Appendix I. Listing of program for variable-boundary tidal model -- Appendix II. Listing of data compression subroutine -- Appendix III. Listing of height and current analysis programs -- Appendix IV. -- Appendix V

Fluid and Halide Melt Inclusions of Magmatic Origin in the Ultramafic and Lower Banded Series, Stillwater Complex, Montana, USA

Fluid and melt inclusions trapped in igneous rocks below the platinum-group element (PGE)-rich J-M reef in the Stillwater Complex, Montana provide a physiochemical record of a continuum of high P-T magmatic-hydrothermal and low P-T metamorphic events. Magmatic-hydrothermal volatiles ranged from NaCl-dominated halide melts (>82 wt % NaClequiv) to more complex Na-Ca-K-Fe-Mn-Ba-Si-Al-Cl brines (28-79 wt % NaClequiv) that were trapped simultaneously with a moderate density carbonic fluid (CO2 ± CH4). Early primary inclusions containing immiscible brine and carbonic fluid were trapped in the granophyric albite-quartz core of a zoned pegmatite body in the Gabbronorite I unit at T of ∼ 700-715°C, and P between 4·3 and 5·6 kbar. The pegmatitic body crystallized from a fluid-saturated residual silicate liquid that was channeled through the cooling igneous stratigraphy. Approximately 500 m stratigraphically below the pegmatite, in the Ultramafic Series, early halide melt inclusions representing samples of formerly molten NaCl were trapped in unaltered primary olivine over a minimum range in temperature of 660-800°C. In the same olivine that hosts the halide melt inclusions, secondary brine inclusions with a composition similar to brines in the pegmatite were trapped over a minimum temperature range of 480-640°C. As hydrothermal activity continued during post-solidus cooling of the intrusion, quartz precipitation in the vuggy core of the pegmatite body trapped post-magmatic, immiscible brine and carbonic fluid inclusion assemblages that record a progressive decrease in fluid salinity, T and confining P from lithostatic to near-hydrostatic conditions. Late secondary inclusions containing regional metamorphic fluids were trapped in quartz in the pegmatite after cooling to zeolite-facies conditions. The late metamorphic fluids were low to moderate salinity, CaCl2-MgCl2-H2O solutions. Hydrous salt melts, magmatic brines, and non aqueous (carbonic) fluids may have coexisted and interacted throughout much of the late crystallization and post-magmatic history of the Stillwater Complex. Hence, the potential for interaction between exsolved magmatic volatiles and grain boundary-hosted sulfide minerals below the J-M reef at near-solidus temperatures, and the post-magmatic modification of the J-M reef PGE ore compositions by hydrothermal fluids are strongly indicate

Atmospheric conditions and their effect on ball-milled magnesium diboride

Magnesium diboride bulk pellets were fabricated from pre-reacted MgB2 powder ball milled with different amounts of exposure to air. Evidence of increased electron scattering including increased resistivity, depressed Tc, and enhanced Hc2 of the milled and heat treated samples were observed as a result of increased contact with air. These and other data were consistent with alloying with carbon as a result of exposure to air. A less clear trend of decreased connectivity associated with air exposure was also observed. In making the case that exposure to air should be considered a doping process, these results may explain the wide varibability of "undoped" MgB2 properties extant in the literature.Comment: Work presented at ASC 2006 in Seattl

Nanoscale grains, high irreversibility field, and large critical current density as a function of high energy ball milling time in C-doped magnesium diboride

Magnesium diboride (MgB2) powder was mechanically alloyed by high energy ball milling with C to a composition of Mg(B0.95C0.05)2 and then sintered at 1000 C in a hot isostatic press. Milling times varied from 1 minute to 3000 minutes. Full C incorporation required only 30-60 min of milling. Grain size of sintered samples decreased with increased milling time to less than 30 nm for 20-50 hrs of milling. Milling had a weak detrimental effect on connectivity. Strong irreversibility field (H*) increase (from 13.3 T to 17.2 T at 4.2 K) due to increased milling time was observed and correlated linearly with inverse grain size (1/d). As a result, high field Jc benefited greatly from lengthy powder milling. Jc(8 T, 4.2 K) peaked at > 80,000 A/cm2 with 1200 min of milling compared with only ~ 26,000 A/cm2 for 60 min of milling. This non-compositional performance increase is attributed to grain refinement of the unsintered powder by milling, and to the probable suppression of grain growth by milling-induced MgO nano-dispersions.Comment: 12 pages, 11 figure

Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development

<p>Abstract</p> <p>Background</p> <p>The Gene Ontology project supports categorization of gene products according to their location of action, the molecular functions that they carry out, and the processes that they are involved in. Although the ontologies are intentionally developed to be taxon neutral, and to cover all species, there are inherent taxon specificities in some branches. For example, the process 'lactation' is specific to mammals and the location 'mitochondrion' is specific to eukaryotes. The lack of an explicit formalization of these constraints can lead to errors and inconsistencies in automated and manual annotation.</p> <p>Results</p> <p>We have formalized the taxonomic constraints implicit in some GO classes, and specified these at various levels in the ontology. We have also developed an inference system that can be used to check for violations of these constraints in annotations. Using the constraints in conjunction with the inference system, we have detected and removed errors in annotations and improved the structure of the ontology.</p> <p>Conclusions</p> <p>Detection of inconsistencies in taxon-specificity enables gradual improvement of the ontologies, the annotations, and the formalized constraints. This is progressively improving the quality of our data. The full system is available for download, and new constraints or proposed changes to constraints can be submitted online at <url>https://sourceforge.net/tracker/?atid=605890&group_id=36855</url>.</p

The Sequence Ontology: a tool for the unification of genome annotations

The Sequence Ontology ( SO) is a structured controlled vocabulary for the parts of a genomic annotation. SO provides a common set of terms and definitions that will facilitate the exchange, analysis and management of genomic data. Because SO treats part-whole relationships rigorously, data described with it can become substrates for automated reasoning, and instances of sequence features described by the SO can be subjected to a group of logical operations termed extensional mereology operators

The evolution of imprinting: chromosomal mapping of orthologues of mammalian imprinted domains in monotreme and marsupial mammals.

BACKGROUND: The evolution of genomic imprinting, the parental-origin specific expression of genes, is the subject of much debate. There are several theories to account for how the mechanism evolved including the hypothesis that it was driven by the evolution of X-inactivation, or that it arose from an ancestrally imprinted chromosome. RESULTS: Here we demonstrate that mammalian orthologues of imprinted genes are dispersed amongst autosomes in both monotreme and marsupial karyotypes. CONCLUSION: These data, along with the similar distribution seen in birds, suggest that imprinted genes were not located on an ancestrally imprinted chromosome or associated with a sex chromosome. Our results suggest imprinting evolution was a stepwise, adaptive process, with each gene/cluster independently becoming imprinted as the need arose.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are