Effects of Preservation Methods, Parasites, and Gut Contents of Black Flies (Diptera: Simuliidae) on Polymerase Chain Reaction Products

Molecular analysis of biological specimens usually requires extraction of high-molecular-weight DNA free of foreign DNA contaminants. DNA was extracted from black flies at different life stages that had been preserved by 4 methods: larvae and adults in ethanol, larvae in Carnoy’s solution, adults on card-points, and adults hand-swatted and sun-dried. Using specific primers for the mitochondrial ND4 gene, a 257-bp amplicon was obtained from specimens preserved by ethanol, card-point mounting, and sun-drying. Successful amplification often required DNA dilutions ≥ 1:20 (\u3c1–10 ng). DNA from specimens preserved in Carnoy’s solution (ethanol: acetic acid, 3:1) yielded degraded DNA, resulting in fewer successful amplifications. Parasitic nematodes and, to a lesser extent, gut contents resulted in extra products when amplified with randomly amplified polymorphic DNA (RAPD) primers. Sufficient DNA was extracted from the head of a larva for a successful polymerase chain reaction (PCR), eliminating the need to remove the contaminating gut and parasites

Shell corrections for finite depth potentials with bound states only

A new method of calculating unique values of ground-state shell corrections for finite depth potentials is shown, which makes use of bound states only. It is based on (i) a general formulation of extracting the smooth part from any fluctuating quantity proposed by Strutinsky and Ivanjuk, (ii) a generalized Strutinsky smoothing condition suggested recently by Vertse et al., and (iii) the technique of the Lanczos $\sigma$ factors. Numerical results for some spherical heavy nuclei ($^{132,154}$Sn, $^{180,208}$Pb and $^{298}$114) are presented and compared to those obtained with the Green's function oscillator expansion method.Comment: 5 pages, 2 tables and 3 figures. Accepted in Physics Letters

An adaptive algorithm for n-body field expansions

An expansion of a density field or particle distribution in basis functions which solve the Poisson equation both provides an easily parallelized n-body force algorithm and simplifies perturbation theories. The expansion converges quickly and provides the highest computational advantage if the lowest-order potential-density pair in the basis looks like the unperturbed galaxy or stellar system. Unfortunately, there are only a handful of such basis in the literature which limits this advantage. This paper presents an algorithm for deriving these bases to match a wide variety of galaxy models. The method is based on efficient numerical solution of the Sturm-Liouville equation and can be used for any geometry with a separable Laplacian. Two cases are described in detail. First for the spherical case, the lowest order basis function pair may be chosen to be exactly that of the underlying model. The profile may be cuspy or have a core and truncated or of infinite extent. Secondly, the method yields a three-dimensional cylindrical basis appropriate for studying galaxian disks. In this case, the vertical and radial bases are coupled; the lowest order radial part of the basis function can be chosen to match the underlying profile only in the disk plane. Practically, this basis is still a very good match to the overall disk profile and converges in a small number of terms.Comment: 16 pages, 5 figures, submitted to A

Evaluation of brine-bearing sands of the Frio Formation, Upper Texas Gulf Coast for geologic sequestration of CO2

Bureau of Economic Geolog

TOUGH2 software qualification

TOUGH2 is a numerical simulation code for multi-dimensional coupled fluid and heat flow of multiphase, multicomponent fluid mixtures in porous and fractured media. It belongs to the MULKOM ({open_quotes}MULti-KOMponent{close_quotes}) family of codes and is a more general version of the TOUGH simulator. The MULKOM family of codes was originally developed with a focus on geothermal reservoir simulation. They are suited to modeling systems which contain different fluid mixtures, with applications to flow problems arising in the context of high-level nuclear waste isolation, oil and gas recovery and storage, and groundwater resource protection. TOUGH2 is essentially a subset of MULKOM, consisting of a selection of the better tested and documented MULKOM program modules. The purpose of this package of reports is to provide all software baseline documents necessary for the software qualification of TOUGH2

Numerical modeling of injection and mineral trapping of CO2 withH2S and SO2 in a Sandstone Formation

Carbon dioxide (CO{sub 2}) injection into deep geologic formations could decrease the atmospheric accumulation of this gas from anthropogenic sources. Furthermore, by co-injecting H{sub 2}S or SO{sub 2}, the products respectively of coal gasification or combustion, with captured CO{sub 2}, problems associated with surface disposal would be mitigated. We developed models that simulate the co-injection of H{sub 2}S or SO{sub 2} with CO{sub 2} into an arkose formation at a depth of about 2 km and 75 C. The hydrogeology and mineralogy of the injected formation are typical of those encountered in Gulf Coast aquifers of the United States. Six numerical simulations of a simplified 1-D radial region surrounding the injection well were performed. The injection of CO{sub 2} alone or co-injection with SO{sub 2} or H{sub 2}S results in a concentrically zoned distribution of secondary minerals surrounding a leached and acidified region adjacent to the injection well. Co-injection of SO{sub 2} with CO{sub 2} results in a larger and more strongly acidified zone, and alteration differs substantially from that caused by the co-injection of H{sub 2}S or injection of CO{sub 2} alone. Precipitation of carbonates occurs within a higher pH (pH > 5) peripheral zone. Significant quantities of CO{sub 2} are sequestered by ankerite, dawsonite, and lesser siderite. The CO{sub 2} mineral-trapping capacity of the formation can attain 40-50 kg/m{sup 3} medium for the selected arkose. In contrast, secondary sulfates precipitate at lower pH (pH < 5) within the acidified zone. Most of the injected SO{sub 2} is transformed and immobilized through alunite precipitation with lesser amounts of anhydrite and minor quantities of pyrite. The dissolved CO{sub 2} increases with time (enhanced solubility trapping). The mineral alteration induced by injection of CO{sub 2} with either SO{sub 2} or H{sub 2}S leads to corresponding changes in porosity. Significant increases in porosity occur in the acidified zones where mineral dissolution dominates. With co-injection of SO{sub 2}, the porosity increases from an initial 0.3 to 0.43 after 100 years. However, within the CO{sub 2} mineral-trapping zone, the porosity decreases to about 0.28 for both cases, because of the addition of CO{sub 2} mass as secondary carbonates to the rock matrix. Precipitation of sulfates at the acidification front causes porosity to decrease to 0.23. The limited information currently available on the mineralogy of naturally occurring high-pressure CO{sub 2} reservoirs is generally consistent with our simulations

Software qualification of selected TOUGH2 modules

The purpose of this package of reports is to provide all software baseline documents necessary for the software qualification of the single-phase Gas (EOS1G), Effective Continuum Method (ECM), Saturated/Unsaturated Flow (EOS9), and Radionuclide Transport (T2R3D) modules of TOUGH2, a numerical simulation code for multi-dimensional coupled fluid and heat flow of multiphase, multicomponent fluid mixtures in porous and fractured media. This report contains the following sections: (1) Requirements Specification, (2) Design Description, (3) Software Validation Test Plan and Report, (4) Software User Documentation, and (5) Appendices. These sections comprise sequential parts of the Software Life Cycle, and are not intended to stand alone but should be used in conjunction with the TOUGH User`s Guide (Pruess, 1987), TOUGH2--A General Purpose Numerical Simulator for Multiphase Fluid and Heat Flow (Pruess, 1991), and the above-referenced TOUGH2 software qualification document. The qualification package is complete with the attached Software Identification Form and executable source code for the single-phase Gas, Effective Continuum method, Saturated/Unsaturated Flow, and Radionuclide Transport modules of TOUGH2

Using a (Higher-Order) Magnus Method to Solve the Sturm-Liouville Problem

The main purpose of this paper is to describe techniques for the numerical solution of a Sturm-Liouville equation (in its Schrodinger form) by employing a Magnus expansion. With a suitable method to approximate the highly oscillatory integrals which appear in the Magnus series, high order schemes can be constructed. A method of order ten is presented. Even when the solution is highly-oscillatory, the scheme can accurately integrate the problem using stepsizes typically much larger than the solution "wavelength". This makes the method well suited to be applied in a shooting process to locate the eigenvalues of a boundary value problem