Major Research Areas

Multi-scale THMC simulations of clay-rich media

This research aims to develop a multi-scale simulation framework capable of predicting the coupled thermal-hydraulic-mechanical-chemical (THMC) properties of fine-grained sediments and sedimentary rocks at the continuum scale with fidelity to the molecular scale properties of hydrated clay colloidal assemblages (Fig. 1). Applications include the isolation of high-level radioactive waste, caprock integrity in carbon capture and storage (CCS), and predictions of cohesive sediment transport, subsea mudflows, and geophysical hazards. Key achievements include the development of new MD and CG simulation methodologies to simulate clay colloidal assemblages on scales of nanometers to micrometers and a new CFD simulation framework capable of representing coupled multiphase flow, mechanics, and heat fluxes in clay-rich rocks. More broadly, this work has generated new understanding of colloidal interactions between anisotropic charged particles across water films, including interparticle interaction mechanisms that are not represented in classical theories of colloidal mechanics.

Figure 1. Multiscale simulations of fine-grained sedimentary media. (A) Macroscale simulations use a new THMC coupled framework that captures sediment ductile deformation, including (a) turbidity currents, (b) erosion, and (c) desiccation cracking. A key requirement is accurate constitutive relations for the properties of fine-grained sediments and sedimentary rocks at the scale of the computational grid. (B) Some grid-scale properties are accurately predicted by all-atom MD simulations of hydrated clay colloidal assemblages on a scale of tens of nanometers. Water molecules are not shown. (C) Other properties are sensitive to the collective structure and dynamics of clay colloidal assemblages on a scale of micrometers, which requires CG simulation approaches (here with explicit ions and implicit water).

Key papers since 2021: Jans M.D., Soulaine C., Yang J.Q., Bourg I.C. A micro-continuum physics-based model for cohesive sediment gravity flows across mudslide, mudflow, and turbidity current regimes. Journal of Geophysical Research: Earth Surface, in review (2026). Zheng X., Bourg I.C. A multiscale approach to simulate multiphase non-isothermal flow in deformable porous materials. Water Resources Research 61, e2025WR041300 (2025). Zheng X., Shen X., Bourg I.C. Coarse-grained simulation of colloidal self-assembly, cation exchange, and rheology in Na/Ca smectite clay gels. Journal of Colloid and Interface Science 693, 137573 (2025). Zheng X., Bourg I.C. Nanoscale prediction of the thermal, mechanical, and transport properties of hydrated clay on 10⁶- and 10¹⁵-fold larger length and time scales. ACS Nano 17, 19211-19223 (2023). Shen X., Bourg I.C. Interaction between hydrated smectite clay particles as a function of salinity (0 to 1 M) and counterion type (Na, K, Ca). Journal of Physical Chemistry C 126, 20990-20997 (2022).

Liquid water microphysics in mineral dust and secondary organic aerosols

This research is focused on understanding the microphysical properties of aerosol particles that represent key sources of uncertainty in climate and air quality models. Significant outcomes include the development of MD simulation approaches that accurately predict the hygroscopicity of secondary organic aerosols (SOA), the stability of adsorbed water films on mineral dust aerosols, and the adsorption of organic compounds at water-air interfaces (Fig. 2). A significant side-focus of this work has examined the adsorption of per- and polyfluoroalkyl substances (PFAS) and other organic contaminants at water-air interfaces to help improve understanding of PFAS atmospheric transport and the design of water treatment systems.

Figure 2. Microphysics of secondary organic aerosols. (A) MD simulation prediction of the κ hygroscopicity parameter (from the κ-Köhler theory of aerosol microphysics) of common semi-volatile organics and comparison with experimental measurements and predictions of the AIOMFAC "fragment model". Results show a strong correlation between hygroscopicity (vertical axis) and organic O:C ratio (horizontal axis). (B) MD simulation prediction of the decrease in surface tension associated with adsorption of PFAS molecules (here perfluorohexane sulfonate, PFHxS) at the water-air interface, including comparison with experimental results (shaded blue region). Adsorbed PFAS molecules experience a strong repulsion between their charged head-groups and a strong attraction between their hydrophobic tails. The near-cancelation of these interactions in certain conditions explains why PFAS adsorption at the water-air interface often follows a Langmuir isotherm despite evidence of strong mutual interactions.

Key papers since 2021: Wen J., Li X, Bourg I.C. From bulk hygroscopicity to nanoscale water activity: Breakdown of continuum theories in sub-4 nm secondary organic aerosols. Environmental Science and Technology, in review (2026). Lemay A.C., Bourg I.C. Interactions between per- and polyfluoroalkyl substances (PFAS) at the water-air interface. Environmental Science and Technology 59, 2201-2210 (2025). Li X., Bourg I.C. Hygroscopic growth of adsorbed water films on smectite clay particles. Environmental Science and Technology 58, 1109-1118 (2024). Li X., Bourg I.C. Phase state, surface tension, water activity, and accommodation coefficient of water-organic clusters near the critical size for atmospheric new particle formation. Environmental Science and Technology 57, 13092-13103 (2023). Lemay A.C., Sontarp E.J., Martinez D., Maruri P., Mohammed R., Neapole R., Wiese M., Willemsen J.A.R., Bourg I.C. Molecular dynamics simulation prediction of the partitioning constants (KH, Kiw, Kia) of 82 legacy and emerging organic contaminants at the water-air interface. Environmental Science and Technology 57, 6296-6308 (2023).

Coupled transport in nanoporous and colloidal systems

This research examines the molecular-scale structure and dynamics of water and ions at interfaces and in nanopores to gain insight on the aqueous chemistry and transport properties of nanoporous and colloidal systems. This work has generated new understanding of the structure of the electrical double layer (EDL) at charged mineral-water interface, the dielectric properties of nano-confined water, and the breakdown of mean field theories of EDL phenomena that play important roles in electrochemistry, nanofiltration, and heterogeneous nucleation. An emerging direction of this work examines how space- and time-resolved memory kernels in fluid-filled nanopores shed new light on coupled transport processes such as electro-osmosis, thermo-osmosis, and streaming currents (Fig. 3).

Figure 3. Coupled transport properties of fluid-filled nanopores. (A) Idealized simulated system with charged and uncharged Lennard-Jones spheres (cation, anion, and solvent in blue, red, and white) in a slit-shaped nanopore with negatively charged walls. Instantaneous fluxes of different quantities in directions parallel to the surface (which fluctuate around zero in the system at equilibrium) are resolved in space and time to calculate transport coefficients using appropriate Green-Kubo relations. (B) Given sufficient spatial and temporal resolution, the result is a 4 x 4 matrix of space- and time-resolved memory kernels. Each panel shows how a uniform, instantaneous pulse of one thermodynamic gradient (from left to right: pressure, salt chemical potential, temperature, or electrostatic potential) would cause a transient response in four different fluxes (from top to bottom: fluxes of solution, salt, heat, and ionic current) as a function of time (horizontal axes) and distance from the pore walls (vertical axes). Integration of each panel in space and time recovers the well-known 4 x 4 Onsager coupled transport matrix.

Key papers since 2021: Hoang Ngoc M.-T., Bourg I.C. Resolving coupled transport in space and time from molecular fluctuations in confined fluids. Nature Communications, in review (2026). Zhakiyeva Z., Magnin V., Poulain A., Campillo S., Asta M.P., Besselink R., Gaboreau S., Claret F., Grangeon S., Rudic S., Rols S., Jimenez-Ruiz M., Bourg I.C., Van Driessche A.E.S., Cuello G.J., Fernandez-Martinez A. Water dynamics in calcium silicate hydrates probed by inelastic neutron scattering and molecular dynamics simulations. Cement and Concrete Research 184, 107616 (2024). Underwood T.R., Bourg I.C. Dielectric properties of water in charged nanopores. Journal of Physical Chemistry B 126, 2688-2698 (2022). Wild B., White C.E., Bourg I.C. Molecular dynamics simulations of reverse osmosis in silica nanopores. Journal of Physical Chemistry C 126, 9161-9172 (2022). Lee S.S., Koishi A., Bourg I.C., Fenter P. Ion correlations drive charge overscreening and heterogeneous nucleation at solid-aqueous electrolyte interfaces. Proceedings of the National Academy of Sciences 118, e2105154118 (2021).

Linking soil physics and biogeochemistry

This research aims to understand how soil physics and biogeochemistry impact the abundance of soil organic matter (SOM), a major source of uncertainty in efforts to predict the future of the global carbon cycle in a warming world. The key challenge is that the dynamics of SOM are sensitive to multi-physics coupled processes over a wide range of scales, from the molecular-level stability of mineral-organic associations to the emergence of soil structure to feedbacks between multiphase flow, nutrient transport, redox conditions, and microbially-driven biogeochemical kinetics (Fig. 4). Major outcomes of this work include (i) validation and refinement of the "onion-skin" model of mineral-associated organic matter and (ii) direct microfluidic observations of organic matter accumulation within clay micro-aggregates. As a side-focus, this work also has generated new understanding of the partitioning of organic contaminants in soils and sediments, including the demonstration that PFAS and phthalate ester adsorption on clay surfaces is driven primarily by hydrophobic interactions.

Figure 4. Multi-scale views of mineral-organic associations in soils. (A) MD simulation of a model of SOM in a system containing a clay mineral surface (lower part of the figure), water (middle part), and air (upper part). Water molecules are not shown. Results demonstrate the formation of a discontinuous organic coating stabilized by hydrophobic interactions. (B) Confocal microscopy image of a red-fluorescent bacterial culture grown in the presence of smectite clay aggregates and a green-fluorescent polysaccharide. The image shows polysaccharide accumulation in clay micro-aggregates (green) and microbial colonization of the outer surface of the aggregates (red), illustrating how clay micro-aggregates may protect SOM from microbial respiration.

Key papers since 2021: Underwood T.R., Bourg I.C., Rosso K.M. Mineral-associated organic matter is heterogeneous and structured by hydrophobic, charged, and polar interactions. Proceedings of the National Academy of Sciences 121, e2413216121 (2024). Kleber M., Bourg I.C., Coward E.K., Hansel C.M., Myneni S.C.B., Nunan N. Dynamic interactions at the mineral-organic matter interface. Nature Reviews Earth & Environment 2, 402-421 (2021). Yang J.Q., Zhang X., Bourg I.C., Stone H.A. 4D imaging reveals mechanisms of clay-carbon protection and release. Nature Communications 12, 622 (2021). Willemsen J.A.R., Bourg I.C. Molecular dynamics simulation of the adsorption of per- and polyfluoroalkyl substances (PFASs) on smectite clay. Journal of Colloid and Interface Science 585, 337-346 (2021).

Multi-scale simulations of microbial biofilms

This research leverages our in-house capabilities for multi-scale, multi-physics simulations of soft Earth materials (soils and sediments) and extends them to represent microbial biofilms, including their cohesiveness, complex rheology, and feedbacks between fluid flow, nutrient transport, and biofilm growth and deformation (Fig. 5). This work has yielded a new continuum-scale model capable of predicting the influence of flow on biofilm morphology. At smaller scales, this research includes MD simulations that aim to establish constitutive relations for the microphysical properties (e.g., swelling pressure, permeability, complex rheology) of biopolymer gels, extracellular polymeric substances (EPS), and microbial biofilms.

Figure 5. Multi-scale simulations of microbial biofilms. (A) Continuum-scale simulation of microbial biofilm growth in a microfluidic device in the presence of nutrient-rich water flow from left to right. (B) MD simulations of a polysaccharide gel (Na-alginate) across a range of hydration states (70 to 95% water). Water molecules are not shown.

Key papers since 2021: Agles A.A., Bourg I.C. Structure and dynamics of water in polysaccharide (alginate) solutions and gels explained by the core-shell model. Biomacromolecules 25, 6403-6415 (2024). Agles A., Bourg I.C. Structure-thermodynamic relationship of a polysaccharide gel (alginate) as a function of water content and counterion type (Na vs. Ca). Journal of Physical Chemistry B 127, 1828-1841 (2023). Kurz D.L., Secchi E., Carrillo F.J., Bourg I.C., Stocker R., Jimenez-Martinez J. Competition between growth and shear stress drives intermittency in preferential flow paths in porous media biofilms. Proceedings of the National Academy of Sciences 119, e2122202119 (2022).