Kyriacos Zygourakis

Research Interests:

Cellular and Tissue Engineering

Chemical Reaction Engineering

Education:

Ph.D. University of Minnesota (1981)

Dipl. Chem. Eng., National Technical University, Athens, Greece (1975)

My research interests span several important areas of bioengineering and reaction engineering. Applied mathematics, computer simulations, video microscopy, and digital image processing are integral parts of my research methodology.

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.

In order to better understand these processes, my group is developing 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 Linux 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.

Biochar for Carbon Sequestration and Soil Amendment:

Effective carbon sequestration must be based on sustainable processes that provide safe, stable carbon sinks with enough capacity to sequester a substantial fraction of anthropogenic CO2 emissions. 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) are used to characterize the chemical composition, surface chemistry, pore structure porosity and reactivity of the produced biochars. Finally, we study the ability of biochars to enhance plant growth with a combination of experimental measurements (like cation exchange capacity) and numerical simulations aimed at understanding how biochar properties influence the transport and retention of nutrients in biochar-amended soils.

The ultimate goal of this research effort is to develop and evaluate sustainable processes for large-scale carbon sequestration through bio-char soil amendment.

Sustainable Production of Fuels and Chemicals from Biomass:

We are working to develop a modeling and computational framework that will allow us to rigorously test wide-held assumptions about the sustainability of large-scale production of fuels and chemicals from biomass. Our initial focus is on the development of a computational tool for the optimal design of chemical reactors and separation processes involved in the production of cellulosic ethanol and biodiesel. Particular emphasis is paid on heat integration and the optimal operation of combined heat and power (CHP) units that generate the steam and electricity needed for the purification of biofuels and their co-products. The commercial success of cellulosic ethanol plants, in particular, will depend to a large extent on our ability to design efficient CHP plants. In the case of biodiesel, our work focuses on the analysis of small-scale plants with batch reactors and highly integrated purification systems that can operate in a distributed fashion to maximize the environmental benefit of this biofuel. We also analyze the energy efficiency of biodiesel plants that burn the produced glycerin and unreacted alcohol to meet the energy demands of the biorefinery or to generate and sell electricity.

Selected Publications

1. M. Stamatakis and K. Zygourakis, “Deterministic and Stochastic Population Level Simulations of an Artificial lac Operon Genetic Network,” BMC Bioinformatics, 12:301 (2011).
   
   
2. K. Spetsieris and K. Zygourakis, “Single-Cell Behavior and Population Heterogeneity: An Inverse Modeling Approach for Computing the Intrinsic Physiological State Functions,” Journal of Biotechnology, accepted (2011).
   
   
3. M. Stamatakis and K. Zygourakis, “A Mathematical and Computational Approach for Integrating the Major Sources of Cell Population Heterogeneity,” Journal of Theoretical Biology, 266, 41–61 (2010).
   
   
4. G. Durnin, J. Clomburg, Z. Yeates, P.J.J. Alvarez, K. Zygourakis, P. Campbell and R. Gonzalez, “Understanding and harnessing the microaerobic metabolism of glycerol in Escherichia coli,” Biotechnology and Bioengineering, 103, 148-161 (2009).
   
   
5. G. Cheng, P. Markenscoff and K. Zygourakis, “A 3D Hybrid Model for Tissue Growth: The Interplay Between Cell Population and Mass Transport Dynamics”, Biophysical J., 97, 401-414 (2009).
   
   
6. K. Spetsieris, N. Mantzaris and K. Zygourakis, "A Novel Assay Based on Fluorescence Microscopy and Image Processing for Determining Phenotypic Distributions of Rod-Shaped Bacteria," Biotechnology and Bioengineering, 102, 598-615 (2009).
   
   
7. B. B. Youssef G. Cheng, K. Zygourakis and P. Markenscoff, “Parallel Implementation of a Cellular Automaton Modeling the Growth of Three-Dimensional Tissues,” J. High Performance Computing Applications, 21, 196-209 (2007).
   
   
8. G. Cheng, B. B. Youssef P. Markenscoff and K. Zygourakis, “Cell Population Dynamics Modulate the Rates of Tissue Growth Processes,” Biophysical J., 90, 713-724 (2006).
   
   
9. G. Cheng and K. Zygourakis, “Cell Migration,” Tissue Engineering and Artificial Organs, J. D. Bronzino, Ed., Taylor and Francis, CRC Press (2006).
   
   
10. S. Perkins, II and K. Zygourakis, “Detection and Characterization of Coal and Char Particle Ignitions,” Ind. Eng. Chem. Res. 43, 3085-3091 (2004).
    
    
11. Y. Cai and K. Zygourakis, “A Multi-Scale Transient Model for Combustion of Highly Porous Chars,” Ind. Eng. Chem. Research, 42, 2746-2755 (2003).
    
    

CHEMICAL & BIOMOLECULAR ENGINEERING DEPT. MS-362
Rice University PO Box 1892 Houston, Texas 77251-1892	E-mail: chbe@rice.edu	Phone: (713) 348-4902 FAX:(713) 348-5478