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Comparison of approaches for simulating reactive solute transport involving organic degradation reactions by multiple terminal electron acceptors
Reactive solute transport models are useful tools for analyzing complex geochemical behavior resulting from biodegradation of organic compounds by multiple terminal electron acceptors (TEAPs). The usual approach of simulating the reactions of multiple TEAPs by an irreversible Monod rate law was compared with simulations that assumed a partial local equilibrium or kinetically controlled reactions subject to the requirement that the Gibbs free energy of reaction (Δ G) was either less than zero or less than a threshold value. Simulations were performed using a single organic substrate and O 2 , FeOOH, SO 4 -2 and CO 2 as the terminal electron acceptors. It was assumed that the organic substrate was slowly and completely fermented to CO 2 and H 2 and the H 2 was oxidized by the TEAPs. Simulations using the Monod approach showed that this irreversible rate law forced the reduction of both FeOOH and CO 2 to proceed even when Δ G was positive. This resulted in an over prediction in amount of FeOOH reduced to Fe(II) in parts of the domain and it resulted in large errors in pH. Simulations using mass action kinetics agreed with equilibrium simulations for the case of large rate constants. The extent of reductive dissolution of FeOOH was strongly dependent on the thermodynamic stability of the FeOOH phase. Transport simulations performed assuming that the reactions of the TEAPs stopped when Δ G exceeded a threshold value showed that only simulated H 2 concentrations were affected if the threshold value was the same for each TEAP. Simulated H2 concentrations were controlled by the fastest reaction of the TEAP, but it was common for reactions to occur concomitantly rather than sequentially.
Modeling Np and Pu transport with a surface complexation model and spatially variant sorption capacities: Implications for reactive transport modeling and performance assessments of nuclear waste disposal sites
One-dimensional (1D) geochemical transport modeling is used to demonstrate the effects of speciation and sorption reactions on the ground-water transport of Np and Pu, two redox-sensitive elements. Earlier 1D simulations (Reardon, 1981) considered the kinetically limited dissolution of calcite and its effect on ion-exchange reactions (involving 90 Sr, Ca, Na, Mg and K), and documented the spatial variation of a 90 Sr partition coefficient under both transient and steady-state chemical conditions. In contrast, the simulations presented here assume local equilibrium for all reactions, and consider sorption on constant potential, rather than constant charge, surfaces. Reardon's (1981) seminal findings on the spatial and temporal variability of partitioning (of 90 Sr) are reexamined and found partially caused by his assumption of a kinetically limited reaction. In the present work, sorption is assumed the predominant retardation process controlling Pu and Np transport, and is simulated using a diffuse-double-layer-surface-complexation (DDLSC) model. Transport simulations consider the infiltration of Np- and Pu-contaminated waters into an initially uncontaminated environment, followed by the cleanup of the resultant contamination with uncontaminated water. Simulations are conducted using different spatial distributions of sorption capacities (with the same total potential sorption capacity, but with different variances and spatial correlation structures). Results obtained differ markedly from those that would be obtained in transport simulations using constant K d , Langmuir or Freundlich sorption models. When possible, simulation results (breakthrough curves) are fitted to a constant K d advection–dispersion transport model and compared. Functional differences often are great enough that they prevent a meaningful fit of the simulation results with a constant K d (or even a Langmuir or Freundlich) model, even in the case of Np, a weakly sorbed radionuclide under the simulation conditions. Functional behaviors that cannot be fit include concentration trend reversals and radionuclide desorption spikes. Other simulation results are fit successfully but the fitted parameters ( K d and dispersivity) vary significantly depending on simulation conditions (e.g. “infiltration” vs. “cleanup” conditions). Notably, an increase in the variance of the specified sorption capacities results in a marked increase in the dispersion of the radionuclides. The results presented have implications for the simulation of radionuclide migration in performance assessments of nuclear waste-disposal sites, for the future monitoring of those sites, and more generally for modeling contaminant transport in ground-water environments.
A Visual Basic program to classify sediments based on gravel-sand-silt-clay ratios
Nomenclature describing size distributions is important to geologists because grain size is the most basic attribute of sediments. Traditionally, geologists have divided sediments into four size fractions that include gravel, sand, silt, and clay, and classified these sediments based on ratios of the various proportions of the fractions. Definitions of these fractions have long been standardized to the grade scale described by Wentworth (1922), and two main classification schemes have been adopted to describe the approximate relationship between the size fractions. Specifically, according to the Wentworth grade scale gravel-sized particles have a nominal diameter of ⩾2.0 mm; sand-sized particles have nominal diameters from <2.0 mm to ⩾62.5 μm; silt-sized particles have nominal diameters from <62.5 to ⩾4.0 μm; and clay is <4.0 μm. As for sediment classification, most sedimentologists use one of the systems described either by Shepard (1954) or Folk (1954, 1974). The original scheme devised by Shepard (1954) utilized a single ternary diagram with sand, silt, and clay in the corners to graphically show the relative proportions among these three grades within a sample. This scheme, however, does not allow for sediments with significant amounts of gravel. Therefore, Shepard's classification scheme (Fig. 1) was subsequently modified by the addition of a second ternary diagram to account for the gravel fraction (Schlee, 1973). The system devised by Folk (1954, 1974) is also based on two triangular diagrams (Fig. 2), but it has 23 major categories, and uses the term mud (defined as silt plus clay). The patterns within the triangles of both systems differ, as does the emphasis placed on gravel. For example, in the system described by Shepard, gravelly sediments have more than 10% gravel; in Folk's system, slightly gravelly sediments have as little as 0.01% gravel. Folk's classification scheme stresses gravel because its concentration is a function of the highest current velocity at the time of deposition, together with the maximum grain size of the detritus that is available; Shepard's classification scheme emphasizes the ratios of sand, silt, and clay because they reflect sorting and reworking (Poppe et al., 2000).
A model of Precambrian geology of Kansas derived from gravity and magnetic data
The fabric of the Precambrian geology of Kansas is revealed through inversion of gravity and magnetic data to pseudo-lithology. There are five main steps in the inversion process: (1) reduction of potential-field data to a horizontal plane in the wavenumber domain; (2) separation of the residual anomaly of interest from the regional background, where an assumption is made that the regional anomaly could be represented by some order of polynomial; (3) subtraction of the signal due to the known topography on the Phanerozoic/Precambrian boundary from the residual anomaly (we assume what is left at this stage are the signals due to lateral variation in the Precambrian lithology); (4) inversion of the residual anomaly in the wavenumber domain to density and magnetization distribution in the top part of the Precambrian constrained by the known geologic information; (5) derivation of pseudo-lithology by characterization of density and magnetization. The boundary between the older Central Plains Province to the north and the Southern Granite-Rhyolite Province to the south is clearly delineated. The Midcontinent Rift System appears to widen in central Kansas and involve a considerable portion of southern Kansas. Lithologies in southwestern Kansas appear to change over fairly small areas and include mafic rocks which have not been encountered in drill holes. The texture of the potential field data from southwestern Kansas suggests a history of continental growth by broad extension. Copyright ?? 1996 Elsevier Science Ltd.
An interactive program for computer-aided map design, display, and query: EMAPKGS2
EMAPKGS2 is a user-friendly, PC-based electronic mapping tool for use in hydrogeologic exploration and appraisal. EMAPKGS2 allows the analyst to construct maps interactively from data stored in a relational database, perform point-oriented spatial queries such as locating all wells within a specified radius, perform geographic overlays, and export the data to other programs for further analysis. EMAPKGS2 runs under Microsoft?? Windows??? 3.1 and compatible operating systems. EMAPKGS2 is a public domain program available from the Kansas Geological Survey. EMAPKGS2 is the centerpiece of WHEAT, the Windows-based Hydrogeologic Exploration and Appraisal Toolkit, a suite of user-friendly Microsoft?? Windows??? programs for natural resource exploration and management. The principal goals in development of WHEAT have been ease of use, hardware independence, low cost, and end-user extensibility. WHEAT'S native data format is a Microsoft?? Access?? database. WHEAT stores a feature's geographic coordinates as attributes so they can be accessed easily by the user. The WHEAT programs are designed to be used in conjunction with other Microsoft?? Windows??? software to allow the natural resource scientist to perform work easily and effectively. WHEAT and EMAPKGS have been used at several of Kansas' Groundwater Management Districts and the Kansas Geological Survey on groundwater management operations, groundwater modeling projects, and geologic exploration projects. ?? 1997 Elsevier Science Ltd.
Time-series animation techniques for visualizing urban growth
Time-series animation is a visually intuitive way to display urban growth. Animations of landuse change for the Baltimore-Washington region were generated by showing a series of images one after the other in sequential order. Before creating an animation, various issues which will affect the appearance of the animation should be considered, including the number of original data frames to use, the optimal animation display speed, the number of intermediate frames to create between the known frames, and the output media on which the animations will be displayed. To create new frames between the known years of data, the change in each theme (i.e. urban development, water bodies, transportation routes) must be characterized and an algorithm developed to create the in-between frames. Example time-series animations were created using a temporal GIS database of the Baltimore-Washington area. Creating the animations involved generating raster images of the urban development, water bodies, and principal transportation routes; overlaying the raster images on a background image; and importing the frames to a movie file. Three-dimensional perspective animations were created by draping each image over digital elevation data prior to importing the frames to a movie file.
The future of scientific communication in the earth sciences: The impact of the internet
Publication on paper of research results following peer-review and editing has been the accepted means of scientific communication for several centuries. Today, the continued growth in the volume of scientific literature, the increased unit costs of archiving paper publications, and the rapidly increasing power and availability of electronic technology are creating tremendous pressures on traditional scientific communication. The earth sciences are not immune from these pressures, and the role of the traditional publication as the primary means of communication is rapidly changing. Electronic publications and network technology are radically altering the relationship between interpretative result and the underlying data. Earth science research institutions, including the Kansas Geological Survey, are experimenting with new forms of on-line publication that assure broad access to research and data and improve application of research results to societal problems. ?? 1997 Elsevier Science Ltd.
GSLIB-style programs for discriminant analysis and regionalized classification
Discriminant analysis is a statistical technique used to predict the group membership of a set of multivariate observations, each of which is assumed to arise from one of a set of distinct classes or groups. Each group is characterized by a certain distribution in multivariate space, and group allocations are based on the similarity of each sample to each group. Assuming multivariate normality, generalized distance measures based on the squared Mahalanobis distance from each sample to each group centroid arise as the natural measure of similarity. One can allocate samples to groups either on the basis of minimum generalized distance or, equivalently, maximum posterior probability of group membership. In earth science applications samples are often associated with geographic locations. In this situation regionalized classification can be used to produce a map representing group membership throughout the sampled domain. This can be accomplished by interpolating either generalized distances or membership probabilities from sample locations to regularly spaced grid nodes and comparing resulting grids to produce a classification map. This paper presents a set of GSLIB-style FORTRAN programs for performing discriminant analysis and regionalized classification. The program disco performs discriminant analysis and the programs xmd2cls and prb2cls combine interpolated distances and probabilities, respectively, to create a grid of predicted classifications. In addition, the utility program colbind allows the user to combine selected columns from different GSLIB-style data files into one file. ?? 1997 Elsevier Science Ltd.
Reminiscences of the editor of the Kansas Geological Survey Computer Contributions, 1966-1970 and a byte
A brief history of the Kansas Geological Survey's Computer Contributions is presented along with the people involved in development of the first geological computer freeware.
UCODE, a computer code for universal inverse modeling
This article presents the US Geological Survey computer program UCODE, which was developed in collaboration with the US Army Corps of Engineers Waterways Experiment Station and the International Ground Water Modeling Center of the Colorado School of Mines. UCODE performs inverse modeling, posed as a parameter-estimation problem, using nonlinear regression. Any application model or set of models can be used; the only requirement is that they have numerical (ASCII or text only) input and output files and that the numbers in these files have sufficient significant digits. Application models can include preprocessors and postprocessors as well as models related to the processes of interest (physical, chemical and so on), making UCODE extremely powerful for model calibration. Estimated parameters can be defined flexibly with user-specified functions. Observations to be matched in the regression can be any quantity for which a simulated equivalent value can be produced, thus simulated equivalent values are calculated using values that appear in the application model output files and can be manipulated with additive and multiplicative functions, if necessary. Prior, or direct, information on estimated parameters also can be included in the regression. The nonlinear regression problem is solved by minimizing a weighted least-squares objective function with respect to the parameter values using a modified Gauss-Newton method. Sensitivities needed for the method are calculated approximately by forward or central differences and problems and solutions related to this approximation are discussed. Statistics are calculated and printed for use in (1) diagnosing inadequate data or identifying parameters that probably cannot be estimated with the available data, (2) evaluating estimated parameter values, (3) evaluating the model representation of the actual processes and (4) quantifying the uncertainty of model simulated values. UCODE is intended for use on any computer operating system: it consists of algorithms programmed in perl, a freeware language designed for text manipulation and Fortran90, which efficiently performs numerical calculations.
Multivariate analyses of Erzgebirge granite and rhyolite composition: Implications for classification of granites and their genetic relations
High-precision major, minor and trace element analyses for 44 elements have been made of 329 Late Variscan granitic and rhyolitic rocks from the Erzgebirge metallogenic province of Germany. The intrusive histories of some of these granites are not completely understood and exposures of rock are not adequate to resolve relationships between what apparently are different plutons. Therefore, it is necessary to turn to chemical analyses to decipher the evolution of the plutons and their relationships. A new classification of Erzgebirge plutons into five major groups of granites, based on petrologic interpretations of geochemical and mineralogical relationships (low-F biotite granites; low-F two-mica granites; high-F, high-P2O5 Li-mica granites; high-F, low-P2O5 Li-mica granites; high-F, low-P2O5 biotite granites) was tested by multivariate techniques. Canonical analyses of major elements, minor elements, trace elements and ratio variables all distinguish the groups with differing amounts of success. Univariate ANOVA's, in combination with forward-stepwise and backward-elimination canonical analyses, were used to select ten variables which were most effective in distinguishing groups. In a biplot, groups form distinct clusters roughly arranged along a quadratic path. Within groups, individual plutons tend to be arranged in patterns possibly reflecting granitic evolution. Canonical functions were used to classify samples of rhyolites of unknown association into the five groups. Another canonical analysis was based on ten elements traditionally used in petrology and which were important in the new classification of granites. Their biplot pattern is similar to that from statistically chosen variables but less effective at distinguishing the five groups of granites. This study shows that multivariate statistical techniques can provide significant insight into problems of granitic petrogenesis and may be superior to conventional procedures for petrological interpretation.
Integration of a numerical model and remotely sensed data to study urban/rural land surface climate processes
Simulation of urban/rural land surface climate processes using boundary layer climate models requires accurate input data with regard to surface thermal and radiative properties. The research reported here resulted in development of a procedure to integrate the satellite-derived surface biophysical parameters with a boundary layer climate model for simulating spatial surface energy exchange. The procedure was tested through spatial surface energy balance simulation of an urban/rural landscape in eastern Nebraska. The modeled surface temperature and net radiation were compared to those derived from the concurrent satellite data. The errors of the modeled surface temperature were small, and were mainly attributed to uncertainties in the estimation of surface moisture availability and satellite-derived surface radiant temperature. Modeled net radiation was also in agreement with the values calculated from satellite data. Modeled turbulent heat fluxes were in general agreement as compared to those reported in the literature, but the model tended to overestimate the latent heat flux for most rural land cover types. It was concluded that by incorporation of satellite-derived surface physical parameters into a boundary layer model, simulation of spatial land surface climate processes was much improved. The method and procedures developed from this study can be utilized in other boundary layer climate models.
Shape functions for velocity interpolation in general hexahedral cells
Numerical methods for grids with irregular cells require discrete shape functions to approximate the distribution of quantities across cells. For control-volume mixed finite-element (CVMFE) methods, vector shape functions approximate velocities and vector test functions enforce a discrete form of Darcy's law. In this paper, a new vector shape function is developed for use with irregular, hexahedral cells (trilinear images of cubes). It interpolates velocities and fluxes quadratically, because as shown here, the usual Piola-transformed shape functions, which interpolate linearly, cannot match uniform flow on general hexahedral cells. Truncation-error estimates for the shape function are demonstrated. CVMFE simulations of uniform and non-uniform flow with irregular meshes show first- and second-order convergence of fluxes in the L2 norm in the presence and absence of singularities, respectively.
Dynamics of diffusive bubble growth and pressure recovery in a bubbly rhyolitic melt embedded in an elastic solid
We present a model of gas exsolution and bubble expansion in a melt supersaturated in response to a sudden pressure drop. In our model, the melt contains a suspension of gas bubbles of identical sizes and is encased in a penny-shaped crack embedded in an elastic solid. The suspension is modeled as a three-dimensional lattice of spherical cells with slight overlap, where each elementary cell consists of a gas bubble surrounded by a shell of volatile-rich melt. The melt is then subjected to a step drop in pressure, which induces gas exsolution and bubble expansion, resulting in the compression of the melt and volumetric expansion of the crack. The dynamics of diffusion-driven bubble growth and volumetric crack expansion span 9 decades in time. The model demonstrates that the speed of the crack response depends strongly on volatile diffusivity in the melt and bubble number density and is markedly sensitive to the ratio of crack thickness to crack radius and initial bubble radius but is relatively insensitive to melt viscosity. The net drop in gas concentration in the melt after pressure recovery represents only a small fraction of the initial concentration prior to the drop, suggesting the melt may undergo numerous pressure transients before becoming significantly depleted of gases. The magnitude of pressure and volume recovery in the crack depends sensitively on the size of the input-pressure transient, becoming relatively larger for smaller-size transients in a melt containing bubbles with initial radii less than 10 - 5 m. Amplification of the input transient may be large enough to disrupt the crack wall and induce brittle failure in the rock matrix surrounding the crack. Our results provide additional basis for the interpretation of volume changes in the magma conduit under Popocatépetl Volcano during Vulcanian degassing bursts in its eruptive activity in April–May 2000.
Persistent earthquake clusters and gaps from slip on irregular faults
Earthquake-producing fault systems like the San Andreas fault in California show self-similar structural variation 1 ; earthquakes cluster in space, leaving aseismic gaps between clusters. Whether gaps represent overdue earthquakes or signify diminished risk is a question with which seismic-hazard forecasters wrestle 1 , 2 , 3 , 4 , 5 . Here I use spectral analysis of the spatial distribution of seismicity along the San Andreas fault (for earthquakes that are at least 2 in magnitude), which reveals that it obeys a power-law relationship, indicative of self-similarity in clusters across a range of spatial scales. To determine whether the observed clustering of earthquakes is the result of a heterogeneous stress distribution, I use a finite-element method to simulate the motion of two rigid blocks past each other along a model fault surface that shows three-dimensional complexity on the basis of mapped traces of the San Andreas fault. The results indicate that long-term slip on the model fault generates a temporally stable, spatially variable distribution of stress that shows the same power-law relationship as the earthquake distribution. At the highest rates of San Andreas fault slip (40 mm yr −1 ), stress patterns produced are stable over a minimum of 25,000 years before the model fault system evolves into a new configuration. These results suggest that although gaps are not immune to rupture propagation they are less likely to be nucleation sites for earthquakes.
Decreased abundance of crustose coralline algae due to ocean acidification
Owing to anthropogenic emissions, atmospheric concentrations of carbon dioxide could almost double between 2006 and 2100 according to business-as-usual carbon dioxide emission scenarios 1 . Because the ocean absorbs carbon dioxide from the atmosphere 2, 3, 4 , increasing atmospheric carbon dioxide concentrations will lead to increasing dissolved inorganic carbon and carbon dioxide in surface ocean waters, and hence acidification and lower carbonate saturation states 2, 5 . As a consequence, it has been suggested that marine calcifying organisms, for example corals, coralline algae, molluscs and foraminifera, will have difficulties producing their skeletons and shells at current rates 6, 7 , with potentially severe implications for marine ecosystems, including coral reefs 6, 8, 9, 10, 11 . Here we report a seven-week experiment exploring the effects of ocean acidification on crustose coralline algae, a cosmopolitan group of calcifying algae that is ecologically important in most shallow-water habitats 12, 13, 14 . Six outdoor mesocosms were continuously supplied with sea water from the adjacent reef and manipulated to simulate conditions of either ambient or elevated seawater carbon dioxide concentrations. The recruitment rate and growth of crustose coralline algae were severely inhibited in the elevated carbon dioxide mesocosms. Our findings suggest that ocean acidification due to human activities could cause significant change to benthic community structure in shallow-warm-water carbonate ecosystems.
Recent acceleration of biomass burning and carbon losses in Alaskan forests and peatlands
Climate change has increased the area affected by forest fires each year in boreal North America. Increases in burned area and fire frequency are expected to stimulate boreal carbon losses. However, the impact of wildfires on carbon emissions is also affected by the severity of burning. How climate change influences the severity of biomass burning has proved difficult to assess. Here, we examined the depth of ground-layer combustion in 178 sites dominated by black spruce in Alaska, using data collected from 31 fire events between 1983 and 2005. We show that the depth of burning increased as the fire season progressed when the annual area burned was small. However, deep burning occurred throughout the fire season when the annual area burned was large. Depth of burning increased late in the fire season in upland forests, but not in peatland and permafrost sites. Simulations of wildfire-induced carbon losses from Alaskan black spruce stands over the past 60 years suggest that ground-layer combustion has accelerated regional carbon losses over the past decade, owing to increases in burn area and late-season burning. As a result, soils in these black spruce stands have become a net source of carbon to the atmosphere, with carbon emissions far exceeding decadal uptake.