Quadrature conductivity: A quantitative indicator of bacterial abundance in porous media

The abundance and growth stages of bacteria in subsurface porous media affect the concentrations and distributions of charged species within the solid-solution interfaces. Therefore, spectral induced polarization (SIP) measurements can be used to monitor changes in bacterial biomass and growth stage. Our goal was to gain a better understanding of the SIP response of bacteria present in a porous material. Bacterial cell surfaces possess an electric double layer and therefore become polarized in an electric field. We performed SIP measurements over the frequency range of 0.1–1 kHz on cell suspensions alone and cell suspensions mixed with sand at four pore water conductivities. We used Zymomonas mobilis at four different cell densities (including the background). The quadrature conductivity spectra exhibited two peaks, one around 0.05–0.10 Hz and the other around 1–10 Hz. Because SIP measurements on bacterial suspensions are typically made at frequencies greater than 1 Hz, these peaks have not been previously reported. In the bacterial suspensions in growth medium, the quadrature conductivity at peak I was linearly proportional to the density of the bacteria. For the case of the suspensions mixed with sands, we observed that peak II presented a smaller increase in the quadrature conductivity with the cell density. A comparison of the experiments with and without sand grains illustrated the effect of the porous medium on the overall quadrature conductivity response (decrease in the amplitude and shift of the peaks to the lower frequencies). Our results indicate that for a given porous medium, time-lapse SIP has potential for monitoring changes in bacterial abundance within porous media

Surface complexation models: An evaluation of model parameter estimation using FITEQL and oxide mineral titration data

The ability of surface complexation models (SCMs) to fit sets of titration data as a function of changes in model parameters was evaluated using FITEQL and acid-base titration data of [alpha]-FeOOH, [alpha]-Al2O3, and TiO2. Three SCMs were evaluated: the triple-layer model (TLM), the constant capacitance model (CCM), and the diffuse-layer model (DLM). For all models evaluated, increasing the model input value for the total number of surface sites caused a decrease in the best-fit Log K values of the surface protolysis constants. In the case of the CCM, the best-fit surface protolysis constants were relatively insensitive to changes in the value of the capacitance fitting parameter, C1, particularly for values of C1 greater than 1.2 F/m2. Similarly, the best-fit values of TLM surface electrolyte binding constants were less influenced by changes in the value of C1 when C1 was greater than 1.2 F/m2. For a given C1 value, the best-fit TLM values of the electrolyte binding constants were sensitive to changes in [Delta]pKa up to [Delta]pKa values of 3. For [Delta]pKa values above 3, no changes in the best-fit electrolyte binding constants were observed. Effects of the quality and extent of titration data on the best-fit values for surface constants are discussed for each model. A method is suggested for choosing a unique set of parameter values for each of the models.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/29417/1/0000493.pd

SecurEarth: A Crosscutting Initiative for the Geo- and Environmental Sciences

"..addressing critical energy and environmental problems will probably have a larger societal impact than curing cancer. Now we just have to convince Congress of that." - Steven Chu, Nobel Laureate and Director of the Lawrence Berkeley National Laboratory, in a 2005 presentation at the LBNL "..a new national energy program is essential and must be initiated with the intensity and commitment of the Manhattan Project, and sustained until this problem is solved" "Considering the urgency of the energy problem, the magnitude of the needed scientific breakthroughs, and the historic rate of scientific discovery, current efforts will likely be too little, too late." - 2003, Basic Energy Science Advisory Committee recommendation Over the next several decades, the U.S. will be facing critical decisions regarding extraction and utilization of the Earth’s resources and stewardship of the Earth. Demands for energy (e.g., fossil, geothermal) and useable water supplies, as well as for places and methods to deal with waste products (e.g., carbon dioxide, radioactive waste), are increasing rapidly. Moreover, the demands are usually interdependent and conflicting. Postponing decisions will become increasingly difficult and unpopular. Complex policy decisions (examples?) with long-range consequences that must be made in the near future will depend on several types of information: social, economic, political and scientific. To balance the urgency with which social, economic, and political information will be used, pertinent scientific information must also be readily available, practical, and possessed with high degree of certainty. Therefore, there is a vital need for timely and relevant scientific information related to energy, resource and environmental issues that will enable decision makers to make better decisions related to public policy. SECUREarth was launched several years ago as a proposition by scientists from DOE national laboratories, universities and industry who recognized two fundamental issues related to the role of the earth sciences, particularly subsurface science, in addressing resource and environmental issues. The first is that we are still struggling to make connections between pore-, molecular- and cellular-scale information and the complex, large-scale systems where we most need predictive capabilities. To take advantage of the growing wealth of scientific information about physical, chemical and biological processes we need to facilitate research leading to an understanding of how individual processes are coupled, how whole-systems behave and can be modeled, and how the response of large-scale systems to natural or engineered changes can be reasonably predicted. It will also be important to assess both the level of uncertainty associated with predictions and the potential consequences of that uncertainty, as well as to develop strategies for minimizing that uncertainty. The second issue for SECUREarth is that the rate at which the science related to the earth’s environment is progressing will not produce some of the most critically needed information by the time policy decisions must be made. Therefore, SECUREarth is concerned both with opening new frontiers for the earth sciences, and also with increasing the rate at which the science becomes useful and available to inform decision makers. The vision for SECUREarth is to facilitate the direction of funding from government and industry sources in order t

Hybrid Numerical Methods for Multiscale Simulations of Subsurface Biogeochemical Processes

Many subsurface flow and transport problems of importance today involve coupled non-linear flow, transport, and reaction in media exhibiting complex heterogeneity. In particular, problems involving biological mediation of reactions fall into this class of problems. Recent experimental research has revealed important details about the physical, chemical, and biological mechanisms involved in these processes at a variety of scales ranging from molecular to laboratory scales. However, it has not been practical or possible to translate detailed knowledge at small scales into reliable predictions of field-scale phenomena important for environmental management applications. A large assortment of numerical simulation tools have been developed, each with its own characteristic scale including molecular (e.g., molecular dynamics), microbial (e.g., cellular automata or particle individual-based models), pore (e.g., lattice-Boltzmann, pore network models, and discrete particle methods such as smoothed particle hydrodynamics) and continuum scales (e.g., traditional partial differential equations solved by finite difference or finite element methods). While many problems can be effectively addressed by one of these models at a single scale, some problems may require explicit integration of models across multiple scales. We are developing a hybrid multi-scale subsurface reactive transport modeling framework that integrates models with diverse representations of physics, chemistry and biology at different scales (sub-pore, pore and continuum). The modeling framework is being designed to take advantage of advanced computational technologies including parallel code components using the Common Component Architecture, parallel solvers, gridding, data and workflow management, and visualization. This paper describes the specific methods/codes being used at each scale, techniques used to directly and adaptively couple across model scales, and preliminary results of application to a multi-scale model of mineral precipitation at a solute mixing interface

Advancing Reactive Tracer Methods for Measurement of Thermal Evolution in Geothermal Reservoirs: Final Report

The injection of cold fluids into engineered geothermal system (EGS) and conventional geothermal reservoirs may be done to help extract heat from the subsurface or to maintain pressures within the reservoir (e.g., Rose et al., 2001). As these injected fluids move along fractures, they acquire heat from the rock matrix and remove it from the reservoir as they are extracted to the surface. A consequence of such injection is the migration of a cold-fluid front through the reservoir (Figure 1) that could eventually reach the production well and result in the lowering of the temperature of the produced fluids (thermal breakthrough). Efficient operation of an EGS as well as conventional geothermal systems involving cold-fluid injection requires accurate and timely information about thermal depletion of the reservoir in response to operation. In particular, accurate predictions of the time to thermal breakthrough and subsequent rate of thermal drawdown are necessary for reservoir management, design of fracture stimulation and well drilling programs, and forecasting of economic return. A potential method for estimating migration of a cold front between an injection well and a production well is through application of reactive tracer tests, using chemical whose rate of degradation is dependent on the reservoir temperature between the two wells (e.g., Robinson 1985). With repeated tests, the rate of migration of the thermal front can be determined, and the time to thermal breakthrough calculated. While the basic theory behind the concept of thermal tracers has been understood for some time, effective application of the method has yet to be demonstrated. This report describes results of a study that used several methods to investigate application of reactive tracers to monitoring the thermal evolution of a geothermal reservoir. These methods included (1) mathematical investigation of the sensitivity of known and hypothetical reactive tracers, (2) laboratory testing of novel tracers that would improve method sensitivity, (3) development of a software tool for design and interpretation of reactive tracer tests and (4) field testing of the reactive tracer temperature monitoring concept

Particle Methods for Simulation of Subsurface Multiphase Fluid Flow and Biogeological Processes

Abstract A number of particle models that are suitable for simulating multiphase fluid flow and biogeological processes have been developed during the last few decades. Here we discuss three of them: a microscopic model -molecular dynamics; a mesoscopic model -dissipative particle dynamics; and a macroscopic model -smoothed particle hydrodynamics. Particle methods are robust and versatile, and it is relatively easy to add additional physical, chemical and biological processes into particle codes. However, the computational efficiency of particle methods is low relative to continuum methods. Multiscale particle methods and hybrid (particle-particle and particle-continuum) methods are needed to improve computational efficiency and make effective use of emerging computational capabilities. These new methods are under development Introduction The computational methods used to simulate single-and multi-phase fluid flow can be divided into two general classes: continuum methods and particle methods. Hybrid particle-continuum methods have also been developed, and some models, such as smoothed particle hydrodynamics and lattice Boltzmann models, can be considered to be either continuum or particle methods. Particle models that can be used to simulate single-and multi-phase fluid dynamics include lattice gas model

Coupling Between Flow and Precipitation in Heterogeneous Subsurface Environments and Effects On Contaminant Fate and Transport

Reactive mixing fronts can occur at large scales, e.g. when chemical amendments are injected in wells, or at small scales (pore-scales) when reactive intermediates are being generated in situ at grain boundaries, cell surfaces and adjacent to biofilms. The product of the reactions such as mineral precipitates, biofilms or filtered colloids modifies permeability leading to the complex coupling between flow and reactions and precipitation. The objectives are to determine how precipitates are distributed within large and small scale mixing fronts, how permeability and flow is modified by precipitation, how the mobility of a representative contaminant, strontium, is affected by the precipitation of carbonates, and how subsequent dissolution of the carbonates result in mobilization of Sr and increased flow. The desired outcomes of the project are to help develop methods leading to sequestration of metal contaminants, and to determine how macroscopic field-scale modeling can be applied to predict the outcome of remediation activities

FLUID FLOW, SOLUTE MIXING AND PRECIPITATION IN POROUS MEDIA

Reactions that lead to the formation of mineral precipitates, colloids or growth of biofilms in porous media often depend on the molecular-level diffusive mixing. For example, for the formation of mineral phases, exceeding the saturation index for a mineral is a minimum requirement for precipitation to proceed. Solute mixing frequently occurs at the interface between two solutions each containing one or more soluble reactants, particularly in engineered systems where contaminant degradation or modification or fluid flow are objectives. Although many of the fundamental component processes involved in the deposition or solubilization of solid phases are reasonably well understood, including precipitation equilibrium and kinetics, fluid flow and solute transport, the deposition of chemical precipitates, biofilms and colloidal particles are all coupled to flow, and the science of such coupled processes is not well developed. How such precipitates (and conversely, dissolution of solids) are distributed in the subsurface along flow paths with chemical gradients is a complex and challenging problem. This is especially true in systems that undergo rapid change where equilibrium conditions cannot be assumed, particularly in subsurface systems where reactants are introduced rapidly, compared to most natural flow conditions, and where mixing fronts are generated. Although the concept of dispersion in porous media is frequently used to approximate mixing at macroscopic scales, dispersion does not necessarily describe pore-level or molecular level mixing that must occur for chemical and biological reactions to be possible. An example of coupling between flow, mixing and mineral precipitation, with practical applications to controlling fluid flow or contaminant remediation in subsurface environments is shown in the mixing zone between parallel flowing solutions. Two- and three-dimensional experiments in packed-sand media were conducted where solutions containing calcium and carbonate ions came into contact along a parallel flow boundary and mixed by dispersion and diffusion. The result is the propagation of calcium carbonate precipitates along the solution-solution boundary in the direction of flow. As carbonate precipitates fill the pore space mixing of the two solutions is restricted and therefore precipitation, flow, and transport are coupled. The distribution of carbonate phases is a complex interaction involving precipitation and dissolution kinetics, which are functions of pore-scale saturation indices and solute ratios, heterogeneous vs. homogeneous nucleation and growth mechanisms and changes in porosity and flow. Experimental and modeling results illustrate challenges in understanding the macroscopic and microscopic phenomena that depend on solute mixing, the relevance of molecular and pore-scale processes to the macroscopic behavior, and potential impact on metal mobility in porous media. Mineral precipitation and changes in porosity are simulated at the pore-scale using the Smooth Particle Hydrodynamics method. Macroscopic simulations were performed using discretized, continuum-scale modeling with parameterization representing macroscopic media properties. One of the modeling goals is to use pore-scale simulations to provide the basis for parameterization of macroscopic (more practical) model predictions

Risk Factors for Mycobacterium ulcerans Infection, Southeastern Australia

Epidemiologic evidence shows that mosquitoes play a role in transmission to humans