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• Sara B. Denison, Peixuan Jin, Kyriacos Zygourakis, Thomas P. Senftle*, and Pedro J. J. Alvarez*, “Mechanistic Implications of the Varying Susceptibility of PAHs to Pyro-Catalytic Treatment as a Function of Their Ionization Potential and Hydrophobicity,” Environ. Sci. Technol., 58(30), 13521-13528 (2024). Online Access
  
  
• S. B. Denison, P. Jin, P. Dias da Silva, C. Chu, B. Moorthy, T. P. Senftle, K. Zygourakis*, and P. J. J. Alvarez*, “Pyro-Catalytic Degradation of Pyrene by Bentonite-Supported Transition Metals: Mechanistic Insights and Trade-Offs with Low Pyrolysis Temperature,” Environ. Sci. Technol., 57(38), 14373-14383 (2023) Online Access
  
  
• Sara B. Denison, Priscilla Dias Da Silva, Caroline P. Koester, Pedro J.J.Alvarez, and Kyriacos Zygourakis*, “Clays play a catalytic role in the pyrolytic treatment of crude-oil contaminated soils that is enhanced by ion-exchanged transition metals,” Journal of Hazardous Materials, 437, Article 129295 (2022) Online Access

• Priscilla Dias da Silva, Michael S. Wong and Kyriacos Zygourakis*, "JP-8 Desulfurization by CuNa-Y Zeolite at Elevated Temperatures Has Two Distinct Stages: Chemisorption Followed by Surface Reactions, " Ind. Eng. Chem. Res., 60(40), 14534–14546 (2021) Online Access

• Ye Gao, Priscilla Dias Da Silva, Pedro J. J. Alvarez, and Kyriacos Zygourakis*, "Integrating Thermal Analysis and Reaction Modeling for Rational Design of Pyrolytic Processes to Remediate Soils Contaminated with Heavy Crude Oil,"  Environ. Sci. Technol., 55, 11987-11996 (2021), Online Access 

• Priscilla Dias da Silva, S. K. Samaniego Andrade, Kyriacos Zygourakis*, Michael S. Wong*, “Adsorptive Desulfurization of Liquid Fuels at Elevated Temperatures Using Metal Exchanged Zeolite Y’, Ind. Eng. Chem. Res., 58, 19623−19632 (2019) Online access
  
  
• Ye Gao and Kyriacos Zygourakis*, “Kinetic Study of the Pyrolytic Treatment of Petroleum-Contaminated Soils,” Ind. Eng. Chem. Res., 58, 10829-10843 (2019). Online Access.
  
  
• W. Song, J. E. Vidonish, P. Yu, C. Chu, B. Moorthy, B. Gao, Kyriacos Zygourakis*, and Pedro J. J. Alvarez*, "Pilot-Scale Pyrolytic Remediation of Crude-Oil Contaminated Soil in a Continuously-Fed Reactor: Treatment Intensity Tradeoffs,” Environ. Sci. Technol., 53, 2045−2053 (2019). Online Access
  
  
• J. E. Vidonish, P. J. J. Alvarez, and Kyriacos Zygourakis*, “Pyrolytic Remediation of Oil-Contaminated Soils: Reaction Mechanisms, Soil Changes, and Implications for Treated Soil Fertility,” Ind. Eng. Chem. Res., 57, 3489−3500 (2018). Online Access
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• K. Zygourakis, “Biochar soil amendments for increased crop yields: How to design a “designer” biochar,” AIChE Journal, 63(12), 5425-5437 (2017) Online Access

 

• C.E. Brewer*, E.T. Hall, K. Schmidt-Rohr, D.A. Laird, R.C. Brown, and K. Zygourakis*, “Temperature and Reaction Atmosphere Effects on the Properties of Corn Stover Biochar,” Environmental Progress & Sustainable Energy, 36(3), 696-707 (2017). Online Access
  
  
• P. Venkataraman*, K. Zygourakis, W.G. Chapman, S.L. Wellington, and M. Shammai, “Molecular Insights into Glass Transition in Condensed Core Asphaltenes,” Energy and Fuels, 31(2), 1182–1192 (2017). Online Access
  
  
• J.E. Vidonish*, K. Zygourakis*, C.A. Masiello, G. Sabadell, and P.J.J. Alvarez*, “Thermal Treatment of Hydrocarbon-Impacted Soils: A Review of Technology Innovation for Sustainable Remediation,” J. Engineering, 2 (4), 426-437 (2016). Online Access
  
  
• J. E. Vidonish*, K. Zygourakis*, C. A. Masiello, X. Gao, J. Mathieu, and P. J. J. Alvarez*, "Pyrolytic Treatment and Fertility Enhancement of Soils Contaminated with Heavy Hydrocarbons,” Environmental Science & Technology, 50, 2498−2506 (2016). Online Access
  
  
• L. A. Pyle, W. C. Hockaday, T. Boutton, K. Zygourakis, T. J. Kinney, and C. A. Masiello*, "Chemical and Isotopic Thresholds in Charring: Implications for the Interpretation of Charcoal Mass and Isotopic Data,” Environmental Science and Technology, 49(24), 14057–14064 (2015). Online Access
  
  
• H. Sun, C. E. Brewer, C. A. Masiello, and K. Zygourakis*, “Nutrient Transport in Soils Amended with Biochar: A Transient Model with Two Stationary Phases and Intraparticle Diffusion,” Industrial and Engineering Chemistry Research, 54, 4123–4135 (2015) Online Access
  
  
• C. E. Brewer*, V. J. Chuang, C. A. Masiello, H. Gonnermann, X. Gao, B. Dugan, L. E. Driver, P. Panzacchi, K. Zygourakis, and C. A. Davies, “New approaches to measuring biochar density and porosity,” Biomass and Bioenergy, 66, 176-185 (2014). Online Access
  
  
• C. A. Masiello, Y. Chen, X. Gao, S. Liu, S. Cheng, M. R. Bennett, J. A. Rudgers, D. S. Wagner, K. Zygourakis, and J. J. Silberg*, “Biochar and Microbial Signaling: Production Conditions Determine Effects on Microbial Communication,” Environmental Science & Technology, 47(20), 11496-11503 (2013). Online Access
  
  
• K. Zygourakis*, H. Sun and P. Markenscoff, “A Nanoscale Model for Characterizing the Pore Structure of Solid Reactants with Ordered and Random Pores,” AIChE Journal, 59(9), 3412-3420 (2013). Online Access
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• H. Sun, W.C. Hockaday, C.A. Masiello and K. Zygourakis*, “Multiple Controls on the Chemical and Physical Structure of Biochars,” Industrial and Engineering Chemistry Research, 51 (9), 3587–3597 (2012) Online Access
  
  
• T.J. Kinney, C.A. Masiello*, B. Dugan, W.C. Hockaday, M.R. Dean, K. Zygourakis and R.T. Barnes, “Hydrologic properties of biochars produced at different temperatures,” Biomass and Bioenergy, 41, 34-43 (2012). Online Access
  
  
• A. Cintolesi, J.M. Clomburg, V. Rigou, K. Zygourakis, R. Gonzalez*, “Quantitative analysis of the fermentative metabolism of glycerol in Escherichia coli,” Biotechnology and Bioengineering, 109, 187–198 (2012) DOI: 10.1002/bit.23309. Online Access
  
  
• 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, 158 (3), 80-90 (2012). Online Access
  
  
• M. Stamatakis and K. Zygourakis*, “Deterministic and Stochastic Population Level Simulations of an Artificial lac Operon Genetic Network,” BMC Bioinformatics, 12:301 (2011). Online access
• 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). Online Access
  
  
• 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).
  
  
• G. Cheng, P. Markenscoff and K. Zygourakis*, “A 3D Hybrid Model for Tissue Growth: The Interplay Between Cell Population and Mass Transport Dynamics”, Biophysical Journal, 97, 401-414 (2009).
  
  
• 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).
  
  
• B. B. Youssef, G. Cheng, K. Zygourakis and P. Markenscoff*, “Parallel Implementation of a Cellular Automaton Modeling the Growth of Three-Dimensional Tissues,” Journal of High Performance Computing Applications, 21, 196-209 (2007).
  
  
• G. Cheng, B. B. Youssef P. Markenscoff and K. Zygourakis*, “Cell Population Dynamics Modulate the Rates of Tissue Growth Processes,” Biophysical Journal, 90, 713-724 (2006).
  
  
• G. Cheng and K. Zygourakis*, “Cell Migration,” Biomedical Engineering Handbook: Tissue Engineering and Artificial Organs, J. D. Bronzino, Ed., Taylor and Francis, CRC Press (2006).
  
  
• H. Shin, K. Zygourakis, M. C. Farach-Carson, M. J. Yaszemski, A. G. Mikos*, “Modulation of differentiation and mineralization of marrow stromal cells cultured on biomimetic hydrogels modified with Arg-Gly-Asp containing peptides,” J. Biomed. Mater. Res. Part A, 69A, 535-543 (2004).
  
  
• S. Perkins, II and K. Zygourakis*, “Detection and Characterization of Coal and Char Particle Ignitions,” Ind. Eng. Chem. Res., 43, 3085-3091 (2004).
  
  
• H. Shin, K. Zygourakis, M. C. Farach-Carson, M. J. Yaszemski and A. G. Mikos, "Attachment, proliferation, and migration of marrow stromal osteoblasts cultured on biomimetic hydrogels modified with an osteopontin-derived peptide," Biomaterials, 25, 895–906 (2004).
  
  
• E. Behravesh, K. Zygourakis, and A.G. Mikos, “Adhesion and Migration of Marrow-Derived Osteoblasts on in Situ Crosslinkable Poly(propylene fumarate co-ethylene glycol) Based Hydrogels with a Covalently Linked RGDS Peptide for Bone Tissue Engineering,” J Biomed Mater Res., 65A, 261–271 (2003).
  
  
• Y. Cai and K. Zygourakis*, “A Multi-Scale Transient Model for Combustion of Highly Porous Chars,” Ind. Eng. Chem. Research, 42, 2746-2755 (2003).
  
  
• E. Behravesh, K. Zygourakis, and A.G. Mikos, “Adhesion and Migration of Marrow-Derived Osteoblasts on in Situ Crosslinkable Poly(propylene fumarate co-ethylene glycol) Based Hydrogels with a Covalently Linked RGDS Peptide for Bone Tissue Engineering,” J Biomed Mater Res., 65A, 261–271 (2003).
  
  
• S. Mani, K. Zygourakis and P. Markenscoff*, “Modeling Wound Healing: Effects of Cell Heterogeneity and Tissue Structure,” Procs. 2nd Joint Conference of the IEEE Engineering in Medicine and Biology Society and the Biomedical Engineering Society, IEEE 02CH37392C, 2239-2240 (2002).
  
  
• E. Behravesh, S. Jo, K. Zygourakis and A. G. Mikos , "Synthesis of In Situ Crosslinkable Macroporous Biodegradable Poly(Propylene Fumarate-b-Ethylene Glycol) Hydrogels,” Biomacromolecules, 3, 374-381 (2002).
  
  
• Y. Belgacem, K., Zygourakis and P. Markenscoff, “A Computational Model for Tissue Regeneration and Wound Healing”, Procs. 3rd Chemical Engineering Symposium, Athens, Greece, vol. 2, 1133-1136 (2001).
  
  
• S. Kouvroukoglou, K. C. Dee, R. Bizios, L.V. McIntire and K. Zygourakis*, "Endothelial Cell Migration on Surfaces Modified with Covalently-Bound Adhesive Peptides," Biomaterials, 21, 1725-1733 (2000).
  
  
• A.J. Bergman and K. Zygourakis*, "Migration of lymphocytes on fibronectin-coated surfaces: temporal evolution of migratory parameters," Biomaterials, 20, 2235-2244 (1999).
  
  
• S. Kouvroukoglou, C.L. Lakkis, J.D. Wallace, K. Zygourakis* and D E. Epner, "Bioenergetics of Rat Prostate Cancer Cell Migration," The Prostate, 34, 137-144 (1998).
  
  
• S. Neelamegham and K. Zygourakis*, "A Mathematical Model for the Kinetics of Homotypic Cellular Aggregation under Static conditions," Biophysical Journal, 72, 51-64 (1997).
  
  
• S. Neelamegham and K. Zygourakis*, "A Quantitative Assay for Intercellelular Aggregation," Annals Biomed. Engrg., 25, 180-189 (1997).
  
  
• S. Neelamegham, S.I. Simon and K. Zygourakis*, "Induction of Homotypic Lymphocyte Aggregation: Evidence for a Novel Activation State of the β1 Integrin," J. Leukocyte Biology, 59, 872-882 (1996).
  
  
• K. Zygourakis*, "Quantification and Regulation of Cell Migration," Tissue Engineering, 2(1), 1-16 (1996). Online Access
  
  
• K. Zygourakis* and P. Markenscoff, "Computer-Aided Design of Bioerodible Devices with Optimal Release Characteristics: A Cellular Automata Approach," Biomaterials, 17, 125-135 (1996).
  
  
• Y. Lee, S. Kouvroukoglou, L.V. McIntire and K. Zygourakis*, "A Cellular Automaton Model for the Proliferation of Migrating Contact-Inhibited Cells," Biophysical Journal, 69, 1284- (1995).
  
  
• Y. Lee, P. Markenscoff, L.V. McIntire and K. Zygourakis*, "Characterization of Endothelial cell Locomotion Using a Markov Chain Model," Biochemistry and Cell Biology, 73, 461-472 (1995).
  
  
• Y. Lee, L.V. McIntire and K. Zygourakis*, “Analysis of Endothelial Cell Locomotion and Proliferation: Differential Effects of Motility and Contact Inhibition,” Biotechnology and Bioengineering, 43, 622-634 (1994).
  
  
• Y. Lee, L.V. McIntire and K. Zygourakis*, "Migration and Proliferation Models for Anchorage-dependent, Contact-inhibited Cells," Biomedical Engrg. Appl. Bas. Commun., 6, 92-98 (1994).
  
  
• T. K. Teague, L.L. Munn, K. Zygourakis and B.W. McIntyre, “Analysis of Lymphocyte Activation and Proliferation by Video Microscopy and Digital Imaging,” Cytometry, 14, 772-782 (1993).
  
  
• L.L. Munn, M.W. Glacken, B.W. McIntyre and K. Zygourakis*, “Analysis of Lymphocyte Aggregation Using Digital Image Analysis, ” Journal of Immunological Methods, 166, 11-25 (1993).
  
  
• A. Matzakos and K. Zygourakis*, “Computerized Thermogravimetric Reactor with Video Microscopy Imaging System,” Review of Scientific Instruments, 64(6), 1541-1548 (1993).
  
  
• K. Zygourakis*, R. Bizios and P. Markenscoff, “Proliferation of Anchorage-Dependent Contact-Inhibited Cells. I. Development of Theoretical Models Based on Cellular Automata,” Biotechnology and Bioengineering, 38, 459-470 (1991).
  
  
• K. Zygourakis*, P. Markenscoff and R. Bizios, “Proliferation of Anchorage-Dependent Contact-Inhibited Cells. II. Experimental results and Comparison to Theoretical Model Predictions,” Biotechnology and Bioengineering, 38, 471-479 (1991).
  
  
• K. Zygourakis*, "Development and Temporal Evolution of Erosion Fronts in Bioerodible Controlled Release Devices," Chemical Engineering Science, 45(8), 2359-2366 (1990).