Principal Investigator

At a Glance

An objective of the Bourg group is to resolve the physics of soil carbon storage. Field experiments indicate that the carbon storage capacity of soils increases significantly with their content in smectite clay minerals, but the cause of this relationship is unknown. The Bourg group is using atomistic-level simulations to predict the energetics of clay-organic interaction, the hydrology of clayey soils and sediments, and their dependence on aqueous chemistry. These results will enable more accurate Earth System Model predictions of soil carbon dynamics and inform practical strategies for enhancing the soil carbon sink.

Research Highlight

Soil carbon is the largest pool of carbon near the Earth’s surface, about as large as the atmosphere, biosphere, and surface ocean combined1. This soil carbon pool has important implications for the Earth’s carbon budget. For example, a minor annual increase in soil carbon content (0.2% per year) would effectively balance global CO2 sources and sinks as required by the Paris Agreement. Conversely, increased soil carbon respiration rates in a warming climate could greatly magnify anthropogenic CO2 emissions2.

Efforts to predict, and eventually control, soil carbon content are challenged by a lack of understanding of the relevant physics. An important clue into the fundamental mechanisms is that soil carbon content correlates strongly with the content of certain aluminosilicate clay minerals (smectite, imogolite, allophane). Possible mechanisms for this relation include carbon protection by adsorption on clay surfaces and the distinct hydrology (strong water retention, low permeability) of clay-rich regions within soils. At present, little is known of these fundamental processes and their dependence on temperature, aqueous chemistry, and the structure of the organic compounds. This information is challenging to extract from field studies because of the inherent complexity of soils, but is critical to the development of a predictive understanding of soil carbon.

The Bourg group is using all-atom molecular dynamics (MD) simulations of simple clay-water-organic systems to gain insight into the fundamental controls on soil carbon storage. The research focuses on two major questions: first, how organic molecules interact with clay surfaces and, second, how clay-water and clay-water-organic interactions control the hydrologic properties of soils. The first effort is carried out under the auspices of CMI along with the PEI Grand Challenges initiative. The second effort is supported since 2017 by grants secured by the Bourg group from the US Department of Energy and the US National Science Foundation. The two research efforts are independent, but their results strongly inform each other, and both may prove crucial to understanding the role of fine-grained minerals in soil carbon storage.

A key breakthrough in the first part of this initiative in 2017 is the demonstration that the atomistic-level simulation methodologies developed by the Bourg group accurately predict the adsorption of dissolved gases3 and organic compounds4. The simulations provide detailed information on the energetics of organic adsorption on clay surfaces and intercalation in clay interlayer nanopores (Figure 1.8.1), properties that are thought to enable protection from microbial degradation. The simulations, which solve Newton’s equations of motion for systems of about 105 atoms using semi-empirical models of all relevant interatomic interactions, require about one month of time on hundreds of parallel processors. The main challenge is to develop models of these interatomic interactions that accurately predict the properties of real clay-water-organic systems, a research area in which the Bourg group is actively involved5.

Figure 1.8.1. Snapshot of a simulation cell containing two Ca-smectite clay nanoparticles (1 nm thick particles with 0.6 nm thick interlayer nanopores) in contact with bulk-liquid-like water (0.1 M CaCl2 solution). Clay structural atoms are shown as red, yellow, pink, green, and white spheres (O, Si, Al, Mg, and H, respectively); water molecules are shown as red and white sticks. In the lower half of the figure, the overlain color map shows the free energy landscape as seen by a single molecule of di-ethyl phthalate (DEP). Dark blue regions near the clay basal surfaces indicate free energy wells where DEP is adsorbed by a combination of polar, Van der Waals, and hydrophobic interactions.

The results show that the affinities of phthalates (compounds selected to mimic the average stoichiometry and aromaticity of soil organic matter) for smectite clay surfaces are commensurate with the reported affinity of soil organic leachate for soil clay minerals. The results reveal that polar interactions associated primarily with the carbonyl groups (>C=O) contribute roughly half of the free energy of adsorption of phthalates on clay surfaces. Further simulations and complementary wet-chemical experiments are underway to characterize the influence of organic structure and aqueous chemistry on adsorption for a broader range of organic compounds.

An important breakthrough in the second part of this initiative is the demonstration that methodologies developed in the Bourg group allow simulating systems of tens of clay particles suspended in liquid water. Simulations are underway to predict the hydrology of clay-water mixtures as a function of compaction and aqueous chemistry (Figure 1.8.2). The results are likely to provide insight into the transport properties of clay-rich regions in soils and sediments6.

In addition to providing an advanced understanding of carbon cycling in soils, this initiative will enable more accurate representations of the migration of water and organics in sediments and sedimentary rocks, for example, in basin modeling and CO2-enhanced oil recovery.

Figure 1.8.2. Snapshots of a simulation cell containing 10 Na-smectite particles (10-nm diameter hexagons) suspended in liquid water. Clay particles are shown as red, yellow, pink, green, and white spheres. Exchangeable Na ions are shown as blue spheres. Water molecules are not shown. The system, initially cubic and containing > 1 million atoms, is progressively dehydrated while applying a constant pressure in the vertical direction in a manner designed to mimic the drying of a clay suspension or the burial of clay-rich sediment. Simulation trajectories will be analyzed to determine how microstructure and transport properties vary with water content and aqueous chemistry in the clayey regions of soils and sediments.


1 Lehmann, J. and M. Kleber, 2015. The contentious nature of soil organic matter. Nature. 528(60): 60-68. doi:10.1038/nature16069.

2 Hicks Pries, C.E., C. Castanha, R. Porras, and M.S. Torn, 2017. The whole-soil carbon flux in response to warming. Science, 355(6332): 1420-1423. doi: 10.1126/science.aal1319.

3 Gadikota, G., B. Dazas, G. Rother, M.C. Cheshire, and I.C. Bourg, 2017. Hydrophobic solvation of gases (CO2, CH4, H2, noble gases) in clay interlayer nanopores. J. Phys. Chem. C. 121(47): 26539-26550. doi: 10.1021/acs.jpcc.7b09768.

4 Willemsen, J. and I.C. Bourg, 2017. Molecular dynamics simulation and experimental study of the adsorption of dimethyl phthalate on clay surfaces. Paper presented at the Goldschmidt Conference, Paris, August 2017.

5 Bourg, I.C., S.S. Lee, P. Fenter, and C. Tournassat, 2017. Structure and energetics of the Stern layer at mica-water interfaces. J. Phys. Chem. C. 121(17): 9402-9412. doi: 10.1021/acs.jpcc.7b01828.

6 Bourg, I.C. and J.B. Ajo-Franklin, 2017. Clay, water, and salt: Controls on the permeability of fine-grained sedimentary rocks. Accounts of Chemical Research. 50(9): 2067-2074. doi: 10.1021/acs.accounts.7b00261.