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Controlling Nucleation and Growth - Thrust Area 1


Manipulating the dissolution, nucleation and growth of minerals in the subsurface requires a detailed understanding of these processes and how they are affected by the special characteristics of porous rock media. The objective of Thrust Area 1 is to develop that understanding at the molecular-level, define the role of microbial communities in mediating those processes in reservoir environments and to explore inorganic, biological and biomimetic methods of directing carbonate mineralization in the subsurface.

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Leads and Contacts - Thrust Area 1

Jim DeYoreo

Jim DeYoreo
Thrust Area 1 Lead

Background and Significance

At the shortest length-scale of fluid-rock interactions, thermodynamic potentials and surface reaction kinetics drive processes of nucleation, growth and dissolution strongly influenced by the composition and structure of the fluid phase, the topology and structure of the solid surfaces, and bulk solid composition. In well-mixed bulk systems, the saturation state with respect to the most stable phase defines the thermodynamics and the energetic barriers to reactions between solute ions and solid surfaces control the kinetics in accordance with well-established theoretical models.  However, in geochemical reservoirs, this simple picture is altered by the complex nature of the solid surface, the presence of nanoparticulate phases, and spatial confinement of the fluid phase.  Resultant deviations from the state of lowest free energy can persist over relevant time scales.  But more significantly, under the constraints of a given particle size or porosity distribution, the system can maintain a steady-state coexistence of phases that deviates from bulk equilibrium. 

The differences between bulk systems and fluid-rock reservoirs lead to major deviations from assumptions of classical theories, the consequences of which are yet to be fully understood or codified. The interplay of these molecular- and nanometer-scale effects will lead to pathways of nucleation and growth not be expected based on each taken individually.  As a result, changes in macroscopic behavior will emerge that cannot be understood by considering bulk systems alone. Thus developing a rigorous description of dissolution/precipitation in spatially confined systems with nm-scale grains and pores constitutes the first major goal of the Center’s research.

The ability to seal deep reservoirs and prevent escape of gases and fluids is likely to be the key requirement if geological carbon dioxide sequestration is to become viable.  Thus, the second major goal is to explore three novel approaches that may enable precise control over the spatial and temporal extent of subsurface carbonate mineralization.


We employ synchrotron-based grazing-incidence small angle X-ray scattering and XPS to determine the effects of fluid composition, saturation state, and other properties of the fluid and solid on rates and distributions of nucleation on mineral substrates.  Hydrothermal AFM provides a tool for identifyoing the atomic environment where nucleation occurs and the evolution of nuclei to crystals.  Measurements of trace element signatures and isotopic differentiation via nanoSIMS and ICP mass spec on crystals grown under identical conditions serve as a probe of reaction pathways.  Direct imaging of the evolution of phases during nucleation and subsequent nano-particle aggregation is being pursued through in situ fluid cell TEM.  To develop a predictive capability, these experimental approaches are combined with molecular dynamics simulations of the earliest events in cluster formation at solution-mineral interfaces and mesoscopic simulations consisting of spatially continuous (“off-lattice”) nanoparticle solutes coupled to a discrete solvent field.  The effect of confined geometries in porous media on the formation of initial clusters and their evolution is investigated by probing the impact of mineral interfaces on the structure of the near-surface solution using surface X-ray and neutron reflectivity combined with molecular dynamics simulations.  Finally, the thermodynamics of carbonates, particularly nano-particles and amorphous and hydrated phases, which ultimately drives all nucleation and growth processes, are determined using calorimetric methods.  Surface energies, dependence of polymorph stability on particle size, and the role of surface hydration are all being investigated.

The first approach to manipulating the timing and rate of carbonate nucleation and growth is development of nanoparticle shuttles comprised of alkaline earth oxides or hydroxides, which will provide the cations needed for carbonate precipitation.  A key component of this work will be development of surfactants that enable the synthesis of nanoparticles and prevent their aggregation, but are stable in super-critical CO2 and CO2 rich brines over an adequate timescale.  A number of ligand systems are being investigated for this purpose including typical soap-like compounds as well as synthetic biopolymers.

Our second approach takes its inspiration from the remarkable level of control that biomolecules can exert over timing, location and rates of mineralization.  From our understanding of the stereochemical basis for biomolecule-surface and -solvent interactions for proteins and peptides, we are designing non-natural biopolymers called peptoids that can survive the harsh conditions of CO2-rich fluids. These peptoids are synthesized and their mineralization-directing properties optimized through combinatorial screening methods combined with molecular-scale studies of their control over nucleation and growth.

Our final approach looks to sub-surface extremophile communities as a means of manipulating mineralization. Model extremophiles are being identified in samples from travertine geysers.  Both consortia and single species are incubated under sequestration-like conditions of temperature, pressure, and CO2 amendment in the presence of relevant mineral constituents.  We then use state-of-the-art molecular approaches to uncover interactions among community members and determine the relevant metabolic potentials and cell surface nucleation sites of individual organisms. Using genetic and proteomic methods we also identify the biochemical pathways and catalytic proteins that regulate the kinetics of these processes.

Expected Outcomes

Through the combination of experiment, simulation and theory we will build a molecular-scale understanding of five key features of geologic CO2 in the sub-surface:

Effect of pore curvature, confinement  and additives on solid/liquid interface structure

Impact of pore topology, metal oxide nanoparticles and biopolymers on nucleation

The evolution of phases, dependence on particle size and carbonate levels and effect of pore curvature, metal oxide nanoparticles and biopolymers

The link between near-surface solution structure, nucleus formation and growth kinetics

The interplay of mass transport and surface kinetics in defining interface stability and concentration profiles.

Our long-term goal is to arrive at a stage where, based on a molecular-scale understanding of these mechanisms and controls, we can reliably predict system evolution, the impact of our controls and their utility in sequestration.

Research Team