Current Projects

CLEAR: Nutrient reduction and recovery

CLEAR (Carbon-Loaded Electrochemical Super Retention) is an EPA-funded project exploring nutrient reduction and recovery from agricultural and urban runoff. Carbon-based treatment systems are being developed to improve water quality and support nutrient reuse.

Public EPA project description.

Biofilm dynamics in complex flows

Biofilms grow, change shape, and alter the flow around them. We develop computational methods to study how these changes interact with substrate transport and microbial activity in natural and engineered systems.

In this work, fluid flow and reactive transport are coupled with a cellular automaton representation of multispecies biofilm growth. The method conserves biomass as biofilms spread and captures characteristic biofilm structures, including species stratification. This provides a way to connect biofilm development with the transport processes that influence reactor performance.

Biofilm processes under fluid flow and their representation in computational cells
Biofilm attachment, growth, decay and detachment under fluid flow, with a computational representation of partially occupied cells.
Successive stages of multispecies biofilm growth under two substrate utilization rates
Multispecies biofilm growth under two substrate utilization rates. Successive stages show changes in biofilm shape and species composition.

Related publication: Kim S, Yao YN (2026). A conservative micro-continuum-cellular automaton method for multispecies biofilm dynamics in complex flows. arXiv preprint.

Biofilms and microplastic transport in porous media

Biofilms continually reshape pore spaces and local flow pathways. We use microfluidic experiments to observe how this changing environment affects microplastic transport in porous media.

Biofilm growth and individual particles are tracked within the same pore space. Our results show that streamer-rich biofilms increase particle retention and trapping, while connected flow pathways formed during bioclogging allow more rapid transport. These observations show why biofilm morphology matters when predicting particle mobility in soils and subsurface environments.

Graphical abstract linking biofilm morphology to microplastic transport, retention and trapping
Biofilm morphology controls microplastic retention and transport through porous media.

Video S2: Streamer-rich biofilms

Microplastics move through distributed pore-space pathways and interact with biofilm streamers.
Open video

Video S3: Preferential flow paths

Microplastic transport is concentrated within connected preferential flow paths in the bioclogged medium.
Open video

Related publication: Shi Z, Yao YN (2026). Evolving biofilm morphology controls microplastic transport in porous media. EarthArXiv preprint.