To understand how the geological subsurface responds to profound perturbations, such as the injection of a reactive immiscible fluid, or deep-geological emplacement of nuclear waste, we need to start with an the understanding of the fundamental pore level processes. These processes occur at the scale of a mineral surface in a pore, or of a microbe on that mineral surface, and comprise the molecular-scale processes that link fluid flow, microbiology, and geochemistry. Typically, investigations in this area emphasize a single approach: fluid dynamics at a single spatial scale or the behavior of a simple microbial population under stress. The challenges come in coupling these processes to identify feedback mechanisms, and then upscaling to link with the larger-scale (spatial and temporal) simulations. This effort will require extending our knowledge of interactions at the level of a mineral surface or biofilm, for example, to the level of a community or an isolated ecosystem, or extending our understanding of adsorption from the molecular scale to a dynamic assemblage of mixed mineral surfaces to derive distribution coefficients. Ultimately, this will lead us to the critical parameters needed to model these processes in functional large-scale simulation tools. 

Figure 1. (a) Micro-CT image of quartz column with liquid CO₂ and brine in the pore space. (b) Laser scanning confocal image of biofilm pore clogging in glass-bead column due to a reduced pH. 

Perturbing a stable biogeochemical system in the subsurface will involve two distinct temporal scales of response: the fast reactions associated with the initial disturbance, and the variable time-scale recovery to a long-term steady state. Our challenge is to use experimental simulations to define initial reactions resulting and then predict the longer term outcome. Iterative comparison of pore-scale short-term experimental work with field observations will not only predict long term outcomes, but may answer fundamental longstanding problems regarding diagenesis in sedimentary basins.

Using carbon sequestration as an example, the target reservoir is typically sandstone capped by shale or mudrock seal to inhibit migration of fluids. At the pore scale, the CO₂ will alter mineral surface chemistry, dehydrate clays, alter pH, stimulate geochemical reactions, and modify the microbial community. Such sandstone-shale sequences form the basis for long-standing fundamental scientific problems regarding: 1) mechanisms and scale of elemental transport, 2) kinetics of diagenesis, and 3) consequences of acid addition (CO₂) in geochemical reactions, and 4) effect of diagenesis on fluid transport. In order to successfully utilize such environments for carbon sequestration, or other geological settings for radioactive waste disposal, these fundamental questions must be investigated at a subpore scale where microbes often mediate fluid-mineral interactions and fluid interfaces dominate multi-phase fluid interactions. The pore-scale models must then be expanded to the pore-network and eventually to the basin scale to address multi-phase fluid transport, elemental mobility, and the effects of diagenesis on transport pathways. Adsorption of contaminants to mineral surfaces, in contrast, is largely responsible for the retardation of radionuclides and other chemical species in the subsurface environment. Despite much research effort, the advancement of models that can be used to successfully calculate or predict adsorption of metal ions and other contaminants is still somewhat limited. Obviously, the complex and varied nature of these interactions has prevented geochemists from developing a general and comprehensive model for biogeochemical processes. Nonetheless, bits and pieces of the modeling puzzle have been provided in recent years through molecular simulation. Likewise mineral surfaces are important in the control of microbial processes and the disposition of biofilms. Unfortunately, little is known of the interplay of contaminants or CO₂ species with microbial colonies and mineral surfaces, or, for that matter, of the direct interaction of microbe with a mineral surface.                

How do we characterize the physicochemical environment of a pore?  
 Imaging a pore or pore network is the basic starting point to build experiments or simulations that will interrogate pore-level biogeochemical interactions.

What is the role of mineralogy in buffering change in a disturbed subsurface and what is the in situ reactive surface area?
Mineral surfaces consume acidity, exchange solutes, and act as habitat for microbes. Even at the atomic scale the nature of the mineral surface governs mineral-fluid interactions. The reactive surface area and the in situ reaction kinetics are two of the most critical parameters in understanding the changing rock-water interactions that result from a disturbance.

How does fluid flow influence biogeochemical reactivity and diffusion?
The flow of the multiphase fluid through a pore will ultimately control mass transfer and reaction extent. Dead zones may be hotspots for reactions and may inhibit or promote reactions.

How does a perturbed system influence feedback mechanisms between minerals, fluids, and microbes?
Microorganisms drive subsurface geochemical reactions, and even small perturbations alter the microbial ecology. This will alter mineral-water reactions, while influencing the inhibiting or stimulating microbial populations, which can result in direct microbe-mineral reactions such as mineral precipitates that will alter fluid flow.

What is the molecular nature of the mineral surface in a pore, and how does that influence fluid or chemical processes?
 Mineral surfaces can relax and react in response to interactions with aqueous solutions; heterogeneous reactions are initiated at the surface.

What are the critical parameters for up-scale for simulations?
 This might include reactive surface area, relative proportions of mobile and immobile zones, permeability structure and equations of state for fluids. 

The innovative aspects and the goals of the research focus in Focus Area 1 consists of developing methods at molecular to pore-scales that allow for quantifying fundamental parameters that determine the flow and transport of brine-CO₂ mixtures in media that are biogeochemically and microbially heterogeneous. A solid foundation and an accurate description of these parameters are needed for a robust performance of the continuum to reservoir scale models in predicting the fate of the injected CO₂.  

We will characterize the complexities of multiphase physical and biogeochemical interactions through fundamental experimental research at the pore scale, integrate these with molecular simulations (Figure 2), and provide parameters for upscaling these complexities and their outcomes to larger-scale systems. Our sub-pore- and pore-scale efforts will incorporate complementary simulation, characterization, and experimental techniques in order to best evaluate and transfer the critical thermodynamic and kinetic parameters.

Figure 2. Molecular dynamics simulation results demonstrating supercritical CO₂ (red) solubility in water (blue).

The results of this research will lead to an understanding of how CO₂ flows through and is trapped in  repository rocks inside the pores and how this affects the local to continuum scale microbial and biogeochemical processes. The understanding of these basic physical and chemical at the subporer scale and their integration in larger scale of reservoir simulation, we will then be able to make useful predictions of CO₂ trapping in real geologic media. The results of the research done in Focus Area 1 will provide a foundation and closely link with Focus Area 2 which bridges the subpore-scale science developed in Task 1 and the continuum-scale science developed in Focus Area 3.

Modeling
An accurate energy force field using Molecular Dynamics (MD) simulations to predict the structure and behavior of gaseous and super critical (sc) CO₂, and the mixing properties of CO₂-H₂O-electrolyte systems is being developed, and a fully flexible description of CO₂ is complete. The force field reproduces CO₂ density near the critical point and it was used to simulate the behavior of CO2 in the interlayer of montmorillonite clay, and determined a signature shift in the O=C=O bending mode consistent with experiment. Simulations of 3D flow and transport inside idealized pores have been conducted for single phase scenarios. The results show the presence of 3D eddies that were examined for their effects on permeability and solute transport. It was shown that continuum-scale flow and transport models are valid after more than dozen pores with eddies (Cardenas, 2009). This work is being extended to actual pore geometries generated from high resolution X-ray CT data. We have established a procedure for imaging a high-pressure column with a three phase system (mineral, scCO₂ and H₂O) at a 5 μm resolution in support of pore-scale flow modeling and experimental geochemistry. Reaction path modeling in support of geochemistry experiments described below has demonstrated weaknesses in the current databases leading to over estimation of CO₂ and calcite solubility in water.                                                  

Microbiology
Growth and respiratory responses of Shewanella oneidensis MR-1 to CO₂ as a function of pressure have been investigated. 2 atm of CO₂ inhibits growth and metabolism while 20 atm for 8 hours results in the loss of cell viability. Incubation for only 4 hours in the presence of the mineral dolomite results in cell death and morphological changes in cells. Initial column experiments to examine the influence of biofilm growth on the transport properties of porous media at the pore scale have been designed.  1mm² capillary tubes have been filled with glass beads and inculated with biofilm growing bacteria (initially Pseudomonas fluorescens). Tracer tests to evaluate the bulk hydrologic properties of the column have been performed during each experiment, and confocal imaging of the column provide information on the hydrologic properties and extent and distribution of biofilm growth. A similar experiment configuration and set of analyses were been used to examine the effect of increasing CO₂ partial pressure on biofilm stability and how this in turn affects pore-scale transport processes.                                                                    

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