Our research is driven by our interest for the coupling between the small scale physical, biological and chemical mechanisms underlying the processes that control soil-like systems, characterised by confined fluids flow, transport & mixing. We use and develop laboratory experiments (mostly microfluidics and video-microscopy), numerical simulations and minimal-ingredient theoretical models. The comparison between micro-scale and field data represents a first step in discovering the laws linking the micro-scale processes to the larger scale behavior, which is not direct in general. The upscaling issue is a major component of our research.



Boreholes drilled into the ground represent traditionally the main source of information about subsurface processes and phenomena, due to the opaque nature of soil and rocks. We build two dimensional micro-models analogs of simplified confined media that consist in two parallel (at least one transparent) solid layers separated by a thin gap filled with impermeable solid obstacles, whose size and shape are designed at will using photo-lithography in a range between micrometers to millimetres.

Microbial transport & chemotaxis


Many soil-dwelling microbes respond to chemical gradients collectively migrating along the gradients direction. This behaviour will affect the microbes residence time and transport properties when exposed to heterogeneous pore-scale flows: it results in a increase in their ability to retain position within pore-scale (few microns) chemical hot-spots, increasing the longitudinal dispersion coefficient. Thus, the small scale flows heterogeneity will also likely control the bio-geo-chemical processes that microbes mediate.

Horizontal Gene Transfer in confined micro-structures

Soil microbial communities are exposed to transported portions of DNA, Mobile Genetic Elements (MGE), which in case of environmental stress can be incorporated by the microbes with a consequent appearance of new physiological functions. The mechanisms responsible for such (horizontal) gene transfer are controlled by the environmental conditions. Thus, due to the complexity of small scale confined flow, the predictions based on rates, measured in well-mixed batch reactors, may differ by orders of magnitudes from observations in the field.

Microbial attachment & Biofilm formation

The evolution of biofilm structures within rough fracture or porous media flows is different from the one observed in absence of fluid flow on a flat surface. The heterogeneous flow conditions, the transport of nutrients and the mechanical fluid stresses are coupled to the formation and the evolution of biofilms. For instance, biofilm structures may partially detach from the solid walls to occupy the pore space with importance consequences on fluid flows, nutrient transport and medium clogging.



The biologically-mediated formation of nanoscale oxide minerals happens in confined environments (e.g. riparian zones or soils): it is a critical biogeochemical process that gives rise to biogenic oxides, reactive solid phases in aquatic and soil environments. The dynamics of bio-mineralisation depends on solutes availability and mixing (e.g. oxygen and minerals), microbes communities and biofilms growth and, thus, likely on their coupling with small scale flows. We aim to investigate small scale bio-mineralization dynamics under hydrodynamic conditions where the interaction between solutes, microorganisms, and mineral particles gives rise to complex systems that typically are heterogeneous in space and time. Moreover, we study the sedimentation of microbes suspended in a liquid solution when a bio-mineralization reaction is taking place.

Mixing in confined flows


Despite the low Reynolds number characterising porous media flows, transport and mixing of solutes and microbes suspensions in confined environments is non trivial. While some mixing properties are shared with turbulent and chaotic systems, there are fundamental differences that must be taken into account to properly model and predict the dynamics of mixing in such media, including the presence of solid boundaries, no flow zones and different flow kinetics and distributions.

Displacing reactive fronts


Only when mixed (occupying the same volume), different chemicals and/or microbes can interact and transform: the mixing dynamics resulting from the combined action of diffusion, dispersion, and advective stretching of a reaction front in heterogeneous flows leads to kinetics that can differ by orders of magnitude from those measured in well-mixed batch reactors. For instance, the reactive front invading a confined medium develop a filamentary structure that elongates and eventually coalesce, controlling the overall reaction kinetics.

Confined flow complexity


Flow structures in confined media lead to localised regions and temporal windows for which the transport is qualitatively and quantitatively different from the average. The complexity of confined flow topologies is fundamentally different from the one resulting in open chaotic or turbulent ones and arise from the random spatial organisation of the host medium and the interaction between the mobile (fluid) and non mobile (solid or trapped fluid) part of the system.

Fluid instabilities


The structure of the host medium is not the only source of heterogeneity for flow and transport. Differences in fluid rheological properties, such as density or viscosity, trigger instabilities (i.e. deviations from a stable displacement) at miscible/non-miscible interfaces which contribute to the system heterogeneity at different scales. These instabilities are typically non stationary and characterized by non trivial dynamics, difficult to model.

Diffusion-limited reactions


Reaction kinetics in reaction-diffusion systems may be different from the ones predicted with well-mixed kinetic laws. Spatial species concentration fluctuations in conjunction with diffusion alone can have a dramatic impact on their global reaction kinetics. The presence of segregated islands of reactants leads anomalous reaction kinetics even in simple reaction-diffusion system, like a bimolecular irreversible one: A + B –> C.