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Partnership of Environmental Education and Research-A compilation of student research, 1999-2008

The U.S. Geological Survey (USGS) Tennessee Water Science Center and the College of Engineering and Technology at Tennessee State University developed a Partnership in Environmental Education and Research (PEER) to support environmental research at TSU and to expand the environmental research capabilities of the USGS in Tennessee. The PEER program is driven by the research needs to better define the occurrence, fate, and transport of contaminants in groundwater and surface water. Research in the PEER program has primarily focused on the transport and remediation of organic contamination in karst settings. Research conducted through the program has also expanded to a variety of media and settings. Research areas include contaminant occurrence and transport, natural and enhanced bioremediation, geochemical conditions in karst aquifers, mathematical modeling for contaminant transport and degradation, new methods to evaluate groundwater contamination, the resuspension of bacteria from sediment in streams, the use of bioluminescence and chemiluminescence to identify the presence of contaminants, and contaminant remediation in wetlands. The PEER program has increased research and education opportunities for students in the College of Engineering, Technology, and Computer Science and has provided students with experience in presenting the results of their research. Students in the program have participated in state, regional, national and international conferences with more than 140 presentations since 1998 and more than 40 student awards. The PEER program also supports TSU outreach activities and efforts to increase minority participation in environmental and earth science programs at the undergraduate and graduate levels. TSU students and USGS staff participate in the TSU summer programs for elementary and high school students to promote earth sciences. The 2007 summer camps included more than 130 students from 20 different States and Washington DC.

Tennessee↗

Dimensional effects of inter-phase mass transfer on attenuation of structurally trapped gaseous carbon dioxide in shallow aquifers

Based on experimental evidence and using mathematical modeling, inter-phase mass transfer processes of CO 2 exsolving from and dissolving into water in heterogeneous porous media are investigated under two fundamentally different flow conditions: in a quasi one dimensional vertical column and in a two-dimensional tank with a lateral background water flow, both at laboratory scale. In both cases, the CO 2 dissolved in water under a given overpressure is injected for a certain period at the bottom of the tank, exsolves, and migrates upwards. A layer of fine sand is present in the tanks designed to mimic geological scenarios of accumulation and trapping of exsolved CO 2 in shallow aquifers. Then, clean water is injected and the accumulated CO 2 is dissolved back into the flowing water. The study aims to point out the differences in the mass transfer processes between the quasi-1D and 2D cases using a mathematical model of two-phase compositional flow in heterogeneous porous media calibrated to the experimental datasets, and expose strategies that should be explored in future research. Additionally, temperature variations observed during the 2D experiments allow for analysis of isothermal versus non-isothermal effects on the processes of multiphase CO 2 evolution. The mathematical model is discretized and solved using the mixed hybrid finite element method in 2D that allows for the simulation of both advection- and diffusion-dominated processes accurately.

Journal of Computational Physics↗

A universal Model-R Coupler to facilitate the use of R functions for model calibration and analysis

Mathematical models are useful in various fields of science and engineering. However, it is a challenge to make a model utilize the open and growing functions (e.g., model inversion) on the R platform due to the requirement of accessing and revising the model's source code. To overcome this barrier, we developed a universal tool that aims to convert a model developed in any computer language to an R function using the template and instruction concept of the Parameter ESTimation program (PEST) and the operational structure of the R-Soil and Water Assessment Tool (R-SWAT). The developed tool (Model-R Coupler) is promising because users of any model can connect an external algorithm (written in R) with their model to implement various model behavior analyses (e.g., parameter optimization, sensitivity and uncertainty analysis, performance evaluation, and visualization) without accessing or modifying the model's source code.

Environmental Modelling and Software↗

A direct method for calculating instrument noise levels in side-by-side seismometer evaluations

The subject of determining the inherent system noise levels present in modem broadband closed loop seismic sensors has been an evolving topic ever since closed loop systems became available. Closed loop systems are unique in that the system noise can not be determined via a blocked mass test as in older conventional open loop seismic sensors. Instead, most investigators have resorted to performing measurements on two or more systems operating in close proximity to one another and to analyzing the outputs of these systems with respect to one another to ascertain their relative noise levels. The analysis of side-by-side relative performance is inherently dependent on the accuracy of the mathematical modeling of the test configuration. This report presents a direct approach to extracting the system noise levels of two linear systems with a common coherent input signal. The mathematical solution to the problem is incredibly simple; however the practical application of the method encounters some difficulties. Examples of expected accuracies are presented as derived by simulating real systems performance using computer generated random noise. In addition, examples of the performance of the method when applied to real experimental test data are shown.

Open-File Report↗

Partly cloudy with a chance of lava flows: Forecasting volcanic eruptions in the 21st century

A primary goal of volcanology is forecasting hazardous eruptive activity. Despite much progress over the last century, however, volcanoes still erupt with no detected precursors, lives and livelihoods are lost to eruptive activity, and forecasting the onsets of eruptions remains fraught with uncertainty. Long‐term forecasts are generally derived from the geological and historical records, from which recurrence intervals and styles of activity can be inferred, while shorter‐term forecasts are derived from patterns in monitoring data. Information from geology and monitoring data can be evaluated and combined using statistical analysis, expert elicitation, and conceptual and or mathematical models. Integrative frameworks, such as event trees, combine this diversity of information to produce probabilistic forecasts that can inform the style and scale of the societal response to a potential future eruption. Several developments show promise to revolutionize the utility and accuracy of these forecasts. These include growth in the quantity and quality of multidisciplinary monitoring data, coupled with increases in computing power; machine learning algorithms, which will allow far better utilization of this growing volume of data; and new physiochemical volcano models and data assimilation algorithms, which take advantage of a wide range of monitoring data and realistic physics to better predict the evolution of a given physical state. Although eruption forecasts may never be as generally reliable as weather forecasts, and great caution must be exercised when attempting to predict highly complex volcanic behavior, these and other innovations—particularly when combined in integrative, fully probabilistic forecasting frameworks—should help volcanologists to better issue warnings of volcanic activity on societally relevant time frames.

Hawaii↗

Bayesian Inference: with ecological applications

This text provides a mathematically rigorous yet accessible and engaging introduction to Bayesian inference with relevant examples that will be of interest to biologists working in the fields of ecology, wildlife management and environmental studies as well as students in advanced undergraduate statistics.. This text opens the door to Bayesian inference, taking advantage of modern computational efficiencies and easily accessible software to evaluate complex hierarchical models.

Book↗

User's Guide for Mixed-Size Sediment Transport Model for Networks of One-Dimensional Open Channels

This user's guide describes a mathematical model for predicting the transport of mixed sizes of sediment by flow in networks of one-dimensional open channels. The simulation package is useful for general sediment routing problems, prediction of erosion and deposition following dam removal, and scour in channels at road embankment crossings or other artificial structures. The model treats input hydrographs as stepwise steady-state, and the flow computation algorithm automatically switches between sub- and supercritical flow as dictated by channel geometry and discharge. A variety of boundary conditions including weirs and rating curves may be applied both external and internal to the flow network. The model may be used to compute flow around islands and through multiple openings in embankments, but the network must be 'simple' in the sense that the flow directions in all channels can be specified before simulation commences. The location and shape of channel banks are user specified, and all bedelevation changes take place between these banks and above a user-specified bedrock elevation. Computation of sediment-transport emphasizes the sand-size range (0.0625-2.0 millimeter) but the user may select any desired range of particle diameters including silt and finer (<0.0625 millimeter). As part of data input, the user may set the original bed-sediment composition of any number of layers of known thickness. The model computes the time evolution of total transport and the size composition of bed- and suspended-load sand through any cross section of interest. It also tracks bed -surface elevation and size composition. The model is written in the FORTRAN programming language for implementation on personal computers using the WINDOWS operating system and, along with certain graphical output display capability, is accessed from a graphical user interface (GUI). The GUI provides a framework for selecting input files and parameters of a number of components of the sediment-transport process. There are no restrictions in the use of the model as to numbers of channels, channel junctions, cross sections per channel, or points defining the cross sections. Following completion of the simulation computations, the GUI accommodates display of longitudinal plots of either bed elevation and size composition, or of transport rate and size composition of the various components, for individual channels and selected times during the simulation period. For individual cross sections, the GUI also allows display of time series of transport rate and size composition of the various components and of bed elevation and size composition.

Water-Resources Investigations Report↗

Evaluation of six methods for estimating magnitude and frequency of peak discharges on urban streams in New York

Six methods of estimating peak discharges of urban streams were compared and evaluated for applicability to urban streams in New York. Discharge and frequency values developed from a series of synthesized annual flood records were compared with values obtained from the six methods. The synthesized flood records were computed from rainfall-runoff models of 11 urban basins in three counties across the State. Four of these basins had a sufficient period of record to enable rainfall-runoff modeling of two different 5-year periods so that increases in peak flow due to increased urbanization could also be used for comparison of the six methods. A graphical analysis and three types of mathematical analyses were made to evaluate the closeness of fit and bias of the methods. All methods showed a tendency to overestimate synthetic urban flood-magnitude values, but the two adjust rural flood-frequency estimates on a nationwide basis showed smallest standard errors of estimate and bias. The standard errors for these two methods ranged from 44 to 57 percent over the six recurrence intervals (2, 5, 10, 25, 50, and 100 year), and the bias ranged from +28 to +53 percent. The bias , however, is probably due to errors inherent in using synthetic records and in applying the New York rural flood-frequency equations to urban basins with small drainage areas. (USGS)

Water-Resources Investigations Report↗

Modeling natural gas reservoirs: A simple model

A mathematical model is developed and tested for the production of natural gas with water encroachment and gas entrapment. The model is built on the material and volumetric balance relations, the Schilthuis water drive model, and a gas entrapment mechanism which assumes that the rate of gas entrapment is proportional to the volumetric rate of water influx. This model represents an alternative to the large grid models because of its low computer, maintenance, and manpower costs.

Society of Petroleum Engineers journal↗

Uncertainty estimation for resource assessment-an application to coal

The U.S. Geological Survey is conducting a national assessment of coal resources. As part of that assessment, a geostatistical procedure has been developed to estimate the uncertainty of coal resources for the historical categories of geological assurance: measured, indicated, inferred, and hypothetical coal. Data consist of spatially clustered coal thickness measurements from coal beds and/or zones that cover, in some cases, several thousand square kilometers. Our procedure involved trend removal, an examination of spatial correlation, computation of a sample semivariogram, and fitting a semivariogram model. This model provided standard deviations for the uncertainty estimates. The number of sample points (drill holes) in each historical category also was estimated. Measurement error in the thickness of the coal bed/zone was obtained from the fitted model or supplied exogenously. From this information approximate estimates of uncertainty on the historical categories were computed. We illustrate the methodology using drill hole data from the Harmon coal bed located in southwestern North Dakota. The methodology will be applied to approximately 50 coal data sets.

Mathematical Geology↗

Mathematical model for simulating discharges on the Sabine River between Tatum and Ruliff, Texas

A mathematical model for simulating discharges on the Sabine River between Tatum and Ruliff, TX., was developed to evaluate the effects of release schedules on discharges from the Toledo Bend Reservoir compared to discharges under natural conditions. Using the discharge at Tatum, TX., the rainfall over the basin, and the discharge release schedule for the reservoir, discharge hydrographs for the natural and reservoir-controlled conditions can be computed.

Texas↗

Fluorite solubility equilibria in selected geothermal waters

Calculation of chemical equilibria in 351 hot springs and surface waters from selected geothermal areas in the western United States indicate that the solubility of the mineral fluorite, CaF 2 , provides an equilibrium control on dissolved fluoride activity. Waters that are undersaturated have undergone dilution by non-thermal waters as shown by decreased conductivity and temperature values, and only 2% of the samples are supersaturated by more than the expected error. Calculations also demonstrate that simultaneous chemical equilibria between the thermal waters and calcite as well as fluorite minerals exist under a variety of conditions. Testing for fluorite solubility required a critical review of the thermodynamic data for fluorite. By applying multiple regression of a mathematical model to selected published data we have obtained revised estimates of the p K (10,96), ΔG o f (−280.08 kcal/mole), ΔH o f (−292.59 kcal/mole), S° (16.39 cal/deg/mole) and C o P (16.16 cal/deg/mole) for CaF 2 at 25°C and 1 atm. Association constants and reaction enthalpies for fluoride complexes with boron, calcium and iron are included in this review. The excellent agreement between the computer-based activity products and the revised p K suggests that the chemistry of geothermal waters may also be a guide to evaluating mineral solubility data where major discrepancies are evident.

Geochimica et Cosmochimica Acta↗

Computational considerations for collecting and using data in the equidistant cylindrical map projection and the bounds of sampling geographic data at progressively higher resolution

The Equidistant Cylindrical Map projection is popular with digital modelers and others for storing and processing worldwide data sets because of the simple association of latitude and longitude to cell values or pixels in the resulting grid. This projection does not accurately display area, and the diminished geographic area represented by cells at high latitudes is not often carefully considered. A simple mathematical analysis quantifies the discrepancy in area sampled by cells at different latitudes. The presence of this discrepancy indicates that the use of this projection can induce bias in data sets when both sampling and reporting data. It is demonstrated that as the resolution requirements of input data for models increase, the necessity of providing data to accurately describe smaller cells, particularly at high latitude, will be a challenge.

Techniques and Methods↗

Mathematical simulation of temperatures in deep impoundments: verification tests of the Water Resources Engineers, Inc. model - Horsetooth and Flaming Gorge Reservoirs

Successful use of predictive mathematical models requires verification of the accuracy of the models by applying them to existing situations where the prediction can be compared with reality. A Corps of Engineers' modification of a deep reservoir thermal stratification model developed by Water Resources Engineers, Inc., was applied to two existing Bureau of Reclamation reservoirs for verification. Diffusion coefficients used for the Corps' Detroit Reservoir were found to apply to Horsetooth Reservoir in Colorado, for which very food computer input data were available. The Detroit diffusion coefficients gave a reasonable simulation of Flaming Gorge Reservoir in Wyoming and Utah, which has very complex and variable physical characteristics and for which only average-quality computer input data were available.

Colorado↗

Data requirements for simulation of hydrogeologic effects of liquid waste injection, Harrison and Jackson Counties, Mississippi

Available literature and data were reviewed to quantify data requirements for computer simulation of hydrogeologic effects of liquid waste injection in southeastern Mississippi. Emphasis of each review was placed on quantifying physical properties of current Class I injection zones in Harrison and Jackson Counties. Class I injection zones are zones that are used for injection of hazardous or non-hazardous liquid waste below a formation containing the lowermost underground source of drinking water located within one-quarter of a mile of the injection well. Several mathematical models have been developed to simulate injection effects. The Basic Plume Method was selected because it is commonly used in permit applications, and the Intercomp model was selected because it is generally accepted and used in injection-related research. The input data requirements of the two models were combined into a single data requirement list inclusive of physical properties of injection zones only; injected waste and well properties are not included because such information is site-specific by industry, which is beyond the scope of this report. Results of the reviews of available literature and data indicated that Class I permit applications and standard-reference chemistry and physics texts were the primary sources of information to quantify physical properties of injection zones in Harrison and Jackson Counties. With the exception of a few reports and supplementary data for one injection zone in Jackson County, very little additional information pertaining to physical properties of the injection zones was available in sources other than permit applications and standard-reference texts.

Mississippi↗

Development and application of generalized-least-squares regression models to estimate low-flow duration discharges in Massachusetts

Physically based mathematical models were developed by use of generalized-least-squares regression analyses to estimate long-term 95-, 98-, and 99-percent duration discharges for ungaged streams in Massachusetts. Duration discharges for 61 sites were used in the recession analyses; 37 sites were streamflow-gaging stations and 24 sites were low-flow partial-record stations. The duration discharges were related to basin chacteristics measured from digital data bases, by use of geographic information systems computer software. Significant chacterisfics used in the models were drainage area, area underlain by stratified-drift deposits per unit of stream length in the basin, and a surrogate for the effective head on the aquifer in the stratified-drift deposits, computed by subtracting the minimum basin elevation from the mean basin elevation. Standard errors of prediction were 57.5, 85.6, and 98.5 percent for models for the 95-, 98-, and 99-percent duration discharges, respectively. Model error variances were about 10 times the sampling error variances, indicating that the precision of future models are likely to be improved more by obtaining better measurements of basin characteristics or by adding new sites to the analyses than by collecting more streamflow data at the sites presently used in the analyses. The models were used to predict duration discharges for 35 selected sites in the Concord River, Noah Coastal, South Coastal, Narragansett and Tenmile River Basins. Ninety-perrcent prediction intervals were computed for the estimates at each of the sites, except at sites where values of the independent variables were outside the ranges of those for the sites used in the regression analyses.

Water-Resources Investigations Report↗

Chemical variability in the Lakeview Mountains pluton, southern California batholith: A comparison of the methods of correspondence analysis and extended Q-mode factor analysis

An extended method of Q -mode factor analysis that has been described previously offers a number of important advantages over conventional Q -mode factor analysis and correspondence analysis when applied to compositional data. Among these are the ability to compute the compositions, in the original units of the data, represented by the reference axes. The only special requirement of the data is that the values for each observation sum to a constant. Mathematically derived reference axes, such as the principal-components and varimax axes, commonly represent compositions that are partly negative. Even where no negative values are present, these compositions are comparatively difficult to interpret in petrologic terms and impossible or inappropriate to include in petrogenetic models. A model has been developed for the Lakeview Mountains pluton which employs vectors representing the compositions of melanocratic schlieren, leucocratic schlieren, and inclusions as the reference axes. When the effect of the inclusions is removed, the compositional zoning in the pluton is like that found in otherwise similar plutons in the Sierra Nevada batholith. The genetic implication of the model is that the inclusions were separated from the magma at least in its marginal parts. In the central part of the pluton, the inclusions were either separated to a lesser extent than in the marginal parts, or were reincorporated into the magma.

California↗

Documentation for the “XT3D” option in the Node Property Flow (NPF) Package of MODFLOW 6

This report describes the “XT3D” option in the Node Property Flow (NPF) Package of MODFLOW 6. The XT3D option extends the capabilities of MODFLOW by enabling simulation of fully three-dimensional anisotropy on regular or irregular grids in a way that properly takes into account the full, three-dimensional conductivity tensor. It can also improve the accuracy of groundwater-flow simulations in cases in which the model grid violates certain geometric requirements. Three example problems demonstrate the use of the XT3D option to simulate groundwater flow on irregular grids and through three-dimensional porous media with anisotropic hydraulic conductivity. Conceptually, the XT3D method of estimating flow between two MODFLOW 6 model cells can be viewed in terms of three main mathematical steps: construction of head-gradient estimates by interpolation; construction of fluid-flux estimates by application of the full, three-dimensional form of Darcy’s Law, in which the conductivity tensor can be heterogeneous and anisotropic; and construction of the flow expression by enforcement of continuity of flow across the cell interface. The resulting XT3D flow expression, which relates the flow across the cell interface to the values of heads computed at neighboring nodes, is the sum of terms in which conductance-like coefficients multiply head differences, as in the conductance-based flow expression the NPF Package uses by default. However, the XT3D flow expression contains terms that involve “neighbors of neighbors” of the two cells for which the flow is being calculated. These additional terms have no analog in the conductance-based formulation. When assembled into matrix form, the XT3D formulation results in a larger stencil than the conductance-based formulation; that is, each row of the coefficient matrix generally contains more nonzero elements. The “RHS” suboption can be used to avoid expanding the stencil by placing the additional terms on the right-hand side of the matrix equation and evaluating them at the previous iteration or time step. The XT3D option can be an alternative to the Ghost-Node Correction (GNC) Package. However, the XT3D formulation is typically more computationally intensive than the conductance-based formulation the NPF Package uses by default, either with or without ghost nodes. Before deciding whether to use the GNC Package or XT3D option for production runs, the user should consider whether the conductance-based formulation alone can provide acceptable accuracy for the particular problem being solved.

Techniques and Methods↗