Portrait | Kyriacos Zygouakis

Kyriacos Zygourakis

Chemical and Biomolecular Engineering

Research Areas

Plants show significantly higher germination and growth in pyrolyzed soils when compared to contaminated or incinerated soils.

Untreated Soil A

TPH: 18,000 mg/kg

Soil A Pyrolyzed in rotary kiln at 420ºC and 15 min residence time

TPH: Not Detectable

Turning Oil Spills into

Fertile Soil

Pyrolytic Treatment of Soils Contaminated with Heavy Petroleum Hydrocarbons

Almost 98% of crude oil spills occur on land with an average of 70 spills per day. Without adequate response, the effects of major spills could last for decades. Although bioremediation can contribute to the cleanup of terrestrial spills, it is very difficult to biodegrade weathered heavy hydrocarbons. While current thermal technologies can quickly remove over 99% of the total petroleum hydrocarbons (TPH), they also destroy key soil constituents and adversely affect soil properties such as organic carbon content, water retention, stability and microbial activity. Thus, treated soils become unsuitable for reuse since they cannot support vegetative growth or even provide erosional stability.

To overcome these problems, we have developed a new pyrolysis process that treats soils contaminated with heavy petroleum crudes at temperatures between 400 and 450 C in anoxic atmospheres. The new process reduces TPH and PAH levels to well below regulatory standards by desorbing low molecular weight hydrocarbons and converting the heavy recalcitrant hydrocarbons to char. For example, treatment at 420 C with only 15 min of residence time in a rotary kiln resulted in high removal efficiencies for both total petroleum hydrocarbons (TPH) (99.9%) and polycyclic aromatic hydrocarbons (PAHs) (94.5%). Viability assays with a human bronchial epithelial cell line showed that pyrolytic treatment effectively achieved detoxification of contaminated soil extracts.

Most importantly, however, plant growth studies with Arabidopsis thaliana and Lactuca sativa (Simpson black-seeded lettuce) showed that soils treated with pyrolysis were much more fertile than either the original contaminated soils or soils treated with incineration. Biomass production rates for pyrolyzed soils were 80-900% higher than the rates we measured for contaminated or incinerated soils. These results suggest that soil pyrolysis could become a viable thermal treatment to quickly remediate soils impacted by weathered crude oil while improving their fertility and potentially enhancing revegetation.

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Water-Food-Energy Nexus


Modeling the response of a bed of biochar-amended soil to typical modes of fertilizer applications

Transport of Nitrogen Fertilizers in 

Biochar-amended Soils

Maintaining a sustainable food supply without degrading our environment will require novel engineering approaches for remediating the human disruption of the nitrogen cycle. More than half of the nitrogen fertilizer applied to fields is not available for plant growth due to losses caused by surface runoff, leaching into surface and groundwater, or volatilization. As a result, the increased use of nitrogen (N) fertilizer has been linked to a variety of water and air pollution problems. In addition, the denitrification reactions generate significant amounts of N2O, a major greenhouse gas.

We use computer simulations and experimental studies to elucidate the fundamental mechanisms controlling the transport and reaction of N fertilizers in biochar-amended soils. We are particularly interested in understanding how key biochar properties (porosity, surface chemistry, adsorption capacity) affect water retention, N leaching, the rates of nitrification and denitrification reactions, and the fate of microbial communities that carry out these reactions.

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       National Academy of Engineering: 

Biochar amendments can increase soil fertility

Macropore structure of apple wood biochar (SEM image, 1500X)

Macropore structure of apple wood biochar (SEM image, 10000X)

Biochar amendments can increase 

the water holding capacity of soils

and improve nutrient retention

Producing Biochars with Optimal 

Environmental Properties

Soil amendment with biochar made by pyrolyzing biomass is a promising new approach with the potential to sequester large amounts of atmospheric carbon. At the same time, strong evidence suggests that amending soils with charcoal increases soil fertility, improves soil drainage, and helps manage nitrogen and phosphorus nutrient pollution.

To better understand the fundamental mechanisms controlling biochar formation, our group is working to determine the pyrolysis conditions that lead to highly stable biochars with optimal carbon sequestration capacity, nutrient retention, and water holding capacity. We have developed specialized reactors that allow us to accurately control the pyrolysis conditions and produce biochars from various feedstocks and for a wide range of heating rates, final heat treatment temperatures and pyrolysis atmosphere. Several analytical techniques (NMR, XPS, gas adsorption, thermogravimetry with on-line masss pectroscopy, differential scanning calorimetry) are used to characterize the chemical composition, surface chemistry, pore structure and reactivity of the produced biochars. Finally, we apply dynamic simulations and nonlinear least-squares methods to develop lumped kinetic models that will be used to design optimal reactors for biomass pyrolysis.

The ultimate goal of our research is to develop“feedstock-blind” reactors for biomass pyrolysis. A thorough understanding of the mechanisms controlling biochar formation will allow us to fine-tune and control the operation of a reactor so that each biomass load will be processed with the optimal temperature program required to produce biochar with the desired environmental properties.

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Modulating the growth of engineered tissues


  • Cell differentiation is critical in determining the structure of in vitro cultivated tissues .
  • Boundary and initial conditions also play important roles in determining their growth rates and final structure.

Dynamic Behavior of Cell Populations Growing Under Mass Transport Limitations

Tissue growth in biomimetic scaffolds is strongly influenced by the dynamics and the heterogeneity of cell populations. A significant source of heterogeneity is the depletion of nutrients and growth factors due to transport limitations. Cells slow down, stop dividing or even die when the concentrations of key nutrients and growth factors drop below certain levels in the scaffold interior. As a result, tissue engineers have not yet been able to grow in vitro tissue samples thicker than a few millimeters for metabolically active cells.

We have developed a multi-scale, hybrid framework that integrates biology with mathematical, computational, and experimental tools to study heterogeneous cell populations growing in three-dimensional scaffolds. We use a discrete, stochastic model to describe the population dynamics of migrating, interacting and proliferating cells. The diffusion and consumption of nutrients and growth factors are modeled by partial differential equations that are subject to boundary conditions appropriate for the bioreactors used in each case. These PDEs are solved numerically and the computed concentration profiles are fed to receptor-mediated binding/trafficking models or simplified kinetic expressions (i.e. Monod kinetics) to modulate cell proliferation rates and migration speeds. To meet the significant computational requirements of this model, parallel implementations of the hybrid algorithms have been developed for computer clusters. Finally, video microscopy and digital image analysis are used to experimentally observe the dynamic behavior of cell populations and find how cell migration and proliferation are influenced by the concentrations of nutrients and growth factors in the culture media, as well as by cell-substrate interactions.

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Computational Modeling for in vitro Tissue Cultivation (Advances in Tissue Engineering, 2021)