Our research interests encompass a wide variety of environmental systems, covering spatial scales from micro to kilometers and time scales from seconds to thousands of years. They include:

Early Diagenesis & Redox transition zones
Reconstruction of paleo-environmental conditions based on the sedimentary record requires an understanding of the processes affecting the deposited matter (Bradey 1985). Burial of reduced substances such as organic matter is relevant for the long-term evolution of oxygen in the atmosphere (Berner and Canfield 1989) while on a shorter timescale, coastal eutrophication and contaminant fate are other key issues motivating research in early diagenesis.

Bioirrigation
An ubiqueouis feature in aquatic sediments is the sequential depletion of terminal electron acceptors (oxygen, nitrate, Mn & Fe oxides, sulfate; Froelich et al. 1979). However, particularly in the coastal ocean, sediments can exhibit a high degree of heterogeneity, to a large part due to the presence of benthic fauna. One of the effects of burrowing organisms on sediment biogeochemistry is through their enhancement of transport of both solids and solutes (bioturbation: Middelburg et al. 1997; bioirrigation: Meile et al. 2001, Koretsky et al. 2002). This is particularly important in the coastal ocean, where benthic organisms are most abundant such that bioirrigation can even strongly affect global biogeochemical cycles (Meile and Van Cappellen 2003).

Water column density interfaces
The Orca basin is a depression located on the northern slope of the Gulf of Mexico. The lower 150 m of the basin are filled with a brine which is separated from the overlying sea water by a strong density stratification due to the increase of salinity from 35 to about 260 ‰. The stratification lowers transport rates dramatically, hence increasing the residence time of settling particulate organic matter in the salinity transition zone. Furthermore, resupply of oxygen to this zone is limited. As a result, the oxic-anoxic interface coincides with the salinity transition zone, promoting anaerobic degradation processes, as well as redox reactions involving reduced byproducts of anaerobic degradation such as Mn(II), Fe(II) or sulfide (Van Cappellen et al. 1998). The depth range over which these reactions occur extends over several meters, instead of the centimeter scale redox gradients usually observed in sediments but redox sequences in such stratified water bodies are similar to those encountered in sediments.

Microbial mats
In contrast to the meter-scale redox transition zone in the Orca basin, microbial mats exhibit a layers of distinct chemical characteristics and microbial populations at the microscale. As ancient forms of living communities, microbial mats are of particular interest from a evolution of life perspective.

Land-Ocean Interface
The coastal zone can be considered a filter between the land and the open ocean. Despite the comparatively small areal extent of the coastal ocean, this highly dynamic environment has a major impact on global biogeochemical cycles (MacKenzie et al. 1998, Slomp et al., in prep.).

Salt marsh biogeochemistry
Salt marshes, amongst the most productive ecosystems on Earth, are located at the land-water interface. Due to their large contribution to elemental turnover, they can have a pronounced effect on both quantity and quality of nutrients released to the coastal ocean. Sediment metabolism shows a distinct seasonal pattern, and we are interested in the driving forces determining pathways of organic matter decomposition (Koretsky et al. 2003).

Groundwater & Subterranean Estuary
Subsurface discharge of groundwater to the coastal ocean is a source of nutrients that only recently received significant attention (Moore 1996, 1999). The chemical composition of the groundwater differs from the oceanic waters, which promotes chemical reactions. Hence, not only is one to consider density effects on flow patterns, but also the biogeochemistry in the saltwater transition zone. We have developed 3D-FEM codes that incorporate density driven flow and allow for a flexible reaction network description. The latter will be based on the developments made with a 1D RTM (Spiteri et al. 2004).

Scaling & Heterogeneity
Heterogeneity in both space and time is a characteristic of most natural environments. It depends on the scale of interest which determines the necessary detail required in the model. Comparing results from models of different complexity allows to address the acceptable level of simplicity (e.g. Meile and Van Cappellen, in prep.). Furthermore, interpolation of model results encompassing different spatial scales can lead to establishment of upscaling laws

Micromodels
Models of porous media commonly employ a continuum description of reaction and transport processes, based on the notion of a representative elementary volume. However, if the reactant distribution at the pore scale is inhomogeneous, this can lead to considerable errors in estimates of reaction rates (Raje and Kapoor 2000). We have developed micromodels, explicitly resolving individual grains to address this issue (Meile and Tuncay, submitted).

Microbial metabolism
Microbes are the principle drivers of elemental turnover, as the biologically catalyzed reaction rates often exceed the abiotic chemical transformations by orders of magnitudes. To date, in most reactive transport models, microbes are treated in a very rudimentary fashion, e.g. as black boxes or using a biomass formulation, without taking into account details of their metabolism. However, with the onset of genetics and microbial ecology, a wealth of information becomes available that can be exploited and incorporated in RTMs. For more detailed information on models of cell metabolism see e.g. the Center for Cell and Virus Theory at IUB.

Extreme environments
Novel insight is often found when stepping beyond the normal, and studying processes in settings with extreme external forcings. Furthermore, such places are often of interest if they are thought to constitute modern analogues to ancient or extraterrestrial life.

Cold seeps
Seeps are windows to the deep subsurface. The rapid translocation of reduced substances from depth to the seafloor drives chemical disequilibria, creating unique niches for life which in turn can alter not only the chemical but also the physical environment (e.g. anaerobic oxidation of methane and carbonate precipitation).

Saline Lakes
Mono Lake, a hypersaline lake located in eastern California, is the site of an ongoing MOBS. It's unique chemical composition allows for a predominance of exotic pathways such as As-reduction which at other places are obscured.

Flexible reactive transport modeling environment

Reactive transport models
Many different applications of reactive transport models are based on similar sets of governing equations, as they are typically based on mass conservation:

where F indicates fluxes of C across the surface S and H source and sink terms within the volume V. Eq. 1 can be reformulated into a system of coupled partial differential equations (PDEs), one for each chemical constituent of interest. With fluxes driven by advection and diffusion and R representing reactions, many RTMs solve

(2)

where D, n and v are diffusion coefficient, porosity and advection velocity, respectively. As the reaction network can vary extensively between applications, it is specified symbolically within MAPLE spreadsheets and then combined with numeric FORTRAN algorithms.

Parameterization
A key issue in modeling is not only to set up and solve the governing equations, but to relate the model to the data in an objective way. To that purpose, we employ both local and global optimization algorithms.

For a more detailed description and a web-based user interface see the RTM site at Utrecht University.

References
- Berner, R.A., and Canfield, D.E. 1989 .A new model for atmospheric oxygen over phanerozoic time, Am. J. Sci. 289 , 333-361.
- Bradley, R.S. 1985. Quarternary Paleoclimatology: Methods of Paleoclimate Reconstruction, 472 pp., Allen & Unwin, Boston.
- Froelich P. N., Klinkhammer G. P., Bender M. L., Luedke N. A., Heath G. R., Cullen D., Dauphin P., Hammond D., Hartmann B. and Maynard V. 1979. Early oxidation of organic matter in pelagic sediments of eastern equatorial Atlantic: suboxic diagenesis. Geochim. Cosmochim. Acta 43(7), 1075-1090.
- Koretsky, C., Meile, C. and Van Cappellen, P. 2002. Quantification of bioirrigation using ecological data: A stochastic approach. Geochem. Transactions 3, 17-30.
- Koretsky C. M., Moore C. M., Lowe K. L., Meile C., DiChristina T. J. and Van Capellen P. 2003. Seasonal Oscillation of Microbial Iron and Sulfate Reduction in Saltmarsh Sediments. Biogeochemistry 64, 179-203.
- MacKenzie F. T., Lerman A. and Ver L. M. 1998. Role of the continental margin in the global carbon balance during the past three centuries. Geology 26(5), 423-426.
- Meile, C., Koretsky, C. and Van Cappellen P. 2001. Quantifying bioirrigation in aquatic sediments - An inverse approach. Limnol. Oceanogr. 46(1), 164-177.
- Meile, C. and Tuncay, K. submitted. Scale dependence of reaction rates in porous media.
- Meile, C. and Van Cappellen, P. in prep. Particle age distribution and O₂ exposure time: Time scales in bioturbated sediments.
- Middelburg J. J., Soetaert K. and Herman P. M. 1997. Empirical relationships for use in global diagenetic models. Deep-Sea Research I 44(2), 327-344.
- Moore, W.S. 1996. Large groundwater inputs to coastal waters revealed by Ra-226 enrichments. Nature 380(6575), 612-614.
- Moore, W.S. 1999. The subterranean estuary: a reaction zone of ground water and sea water. Mar. Chem. 65(1-2), 111-125.
- Raje D. S. and Kapoor V. 2000. Experimental study of bimolecular reaction kinetics in porous media. Environ. Sci. Technol. 34(7), 1234-1239.
- Slomp, C.P., Meile, C. and Van Cappellen, P. in prep. The global marine phosphorus cycle: response to ocean anoxia.
- Spiteri C., Regnier P., Van Cappellen P., Slomp C. and Meile C. 2004. Modeling of geochemical processes in an aquifer infiltrated by a septic plume. Water-Rock Interaction 11, 4.
- Van Cappellen P., Viollier E., Roychoudhury A., Clark L., Ingall E., Lowe K. and DiChristina T. 1998. Biogeochemical Cycles of Manganese and Iron at the Oxic-Anoxic Transition of a Stratified Marine Basin (Orca Basin, Gulf of Mexico). Environ. Sci. Technol. 32(19), 2931-2939.