PNG 550
Reactive Transport in the Subsurface

0.1 History of reactive transport modeling

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Reactive transport models have been applied to understand biogeochemical systems for more than three decades (Beaulieu et al., 2011; Brown and Rolston, 1980; Chapman, 1982; Chapman et al., 1982; Lichtner, 1985; Regnier et al., 2013; Steefel et al., 2005; Steefel and Lasaga, 1994). Multi-component RTMs originated in the 1980s based on the theoretical foundation of the continuum model (Lichtner, 1985; Lichtner, 1988). RTM development advanced substantially in the 1990s with the emergence of several extensively-used RTM codes, including Hydrogeochem (Yeh and Tripathi, 1991; Yeh and Tripathi, 1989), CrunchFlow (Steefel and Lasaga, 1994), Flotran (Lichtner et al., 1996), Geochemist’s Workbench (Bethke, 1996), Phreeqc (Parkhurst and Appelo, 1999), Min3p (Mayer et al., 2002), STOMP (White and Oostrom, 2000), TOUGHREACT (Xu et al., 2000), among others (Ortoleva et al., 1987, Bolton, 1996). Several early diagenetic models were developed at similar times, including STEADYSED (Van Cappellen and Wang, 1996), CANDI (Boudreau, 1996), and OMEXDIA (Soetaert et al., 1996). These codes can be easily found through google their names. 

RTMs are distinct from geochemical models that primarily calculate geochemical equilibrium, speciation, and thermodynamic state of a system (Wolery et al., 1990). RTMs also differ from reaction path models (Helgeson, 1968; Helgeson et al., 1969) that represent closed or batch systems without diffusive or advective transport. The major advance of modern RTMs was to couple flow and transport within a full geochemical thermodynamic and kinetic framework (Steefel et al., 2015). 

RTMs have been used across an extensive array of environments and applications (as reviewed in MacQuarrie and Mayer, 2005; Steefel et al., 2005). One primary focus has been in the low-temperature (ca < 100˚C) surface and near-surface environment where “rock meets life”, a region often referred to as the Critical Zone (CZ). Within the critical zone, water, atmosphere, rock, soil, and life interact creating the potential for complex chemical, physical, and biological interactions and responses to external forcing. As illustrated in Figure 0.1, RTMs can simulate a wide range of processes in this environment, including fluid flow (single or multiphase), solute transport (advective, dispersive, and diffusive transport), geochemical reactions (e.g., mineral dissolution and precipitation, ion exchange, surface complexation), and biogeochemical processes (e.g., microbe-mediated redox reactions, biomass growth and decay). 

Schematic representation of the oxidation-reduction zones that may develop in an aquifer- see caption
Figure 0.1. A schematic representation of the oxidation–reduction zones that may develop in an aquifer downstream from an organic-rich landfill. A zone of methanogenesis develops and is followed down gradient progressively by zones of sulfate reduction, dissimilatory iron reduction, denitrification, and aerobic respiration that develop as the plume becomes oxidized through the influx of oxygenated water. Within the iron reduction zone, a pore scale image shows that the influx of dissolved organics provides electrons for iron reduction mediated by a biofilm, with a suite of other reaction products including Fe2+, HCO3-, and OH-, as well as solid phase precipitates, such as siderite or calcite, which end up reducing the porosity and permeability of the material. Sorption of Fe2+ may also occur on clays, displacing other cations originally present on the mineral surface (from Steefel et al., 2005 with permission). 

RTMs with these capabilities have been applied to understand chemical weathering and soil formation in response to various biological, climatic and physical drivers. RTMs have also been essential to address a wide range of questions at the nexus of energy and the environment, including, for example, environmental bioremediation (Bao et al., 2014), natural attenuation (Mayer et al., 2001), geological carbon sequestration (Apps et al., 2010; Brunet et al., 2013; Navarre-Sitchler et al., 2013), and nuclear waste disposal (Saunders and Toran, 1995; Soler and Mader, 2005). Model frameworks have advanced to incorporate heterogeneous characteristics of natural systems to begin to understand the role of spatial heterogeneities in controlling flow and the interaction between water and reacting components (Scheibe et al., 2006; Yabusaki et al., 2011; Liu et al., 2013). With the expansion of isotopes as tracers of mineral-fluid and biologically mediated reactions, recent advances include development of RTMs that allow an explicit treatment of isotopic partitioning due to both kinetic and equilibrium process.

The RTM approach has also been used to investigate subsurface processes at spatial scales ranging from single pores (Kang et al., 2006; Li et al., 2008; Molins et al., 2012) and single cells (Scheibe et al., 2009; Fang et al., 2011), to pore networks and columns (1 -10s centimeters) (Knutson et al., 2005; Li et al., 2006; Yoon et al., 2012; Druhan et al., 2014), and to field scales (1-10’s of meter) (Li et al., 2011), with a few studies at the watershed or catchment scale (100s of meters) (Atchley et al., 2014). Recent weathering studies have linked regional scale reactive transport models (WITCH) to global climate models to understand the role of climate change in controlling weathering (Godderis et al., 2006; Roelandt et al., 2010). Recent model development also includes full coupling between subsurface biogeochemical processes and surface hydrology, land-surface interactions, meteorological and climatic forcings (Bao et al., 2017; Li et al., 2017a). Such coupling has been argued to be important in understanding the complex interactions between processes of interests in different disciplines (Li et al., 2017b).