RELATED PAPERS

MTS Theory and Microbial Thermodynamics

• Dev, S. Katipoglu-Yazan, T., Desmond-Le Quéméner, E. Thermodynamic gamblers: why warming favours microbes that accelerate it. Nature Communications (Under Consideration).
• Leurent, A., & Moscoviz, R. (2022). Modeling a propionate-oxidizing syntrophic coculture using thermodynamic principles. Biotechnology and Bioengineering, 119, 2423–2436. 
• Ugalde-Salas, P., Desmond-Le Quéméner, E., Harmand, J., Rapaport, A., Bouchez, T. (2020). Insights from microbial transition state theory on monod’s affinity constant. Scientific Reports, 10(1), 5323.
• Consistent microbial dynamics and functional community patterns derived from first principles. Delattre, H., Desmond-Le Quéméner, E., Duquennoi, C., Filali, A., Bouchez, T. (2019). The ISME Journal, 13(2), 263-276.
• A thermodynamic theory of microbial growth. Desmond-Le Quéméner, E., Bouchez, T. (2014). The ISME Journal, 8(8):1747-1751.
• Katipoglu-Yazan, T., Dev, S., Desmond-Le Quéméner, E., Bouchez, T., (2023). Data on the influence of temperature on the growth of Escherichia coli in a minimal medium containing glucose as the sole carbon source for the joint computation of growth yields and rates at each temperature from 27 to 45° C. Data in Brief. 48, 109037.
• Soylu, D., Insel, G., Cokgor, E., Katipoglu-Yazan, T., Modeling Influence of Chronic Nickel Exposure on Nitrification Kinetics: Microbial Transition State Theory versus Activated Sludge Model.CESEE, 4th International Conference on Chemical, Energy Science and Environmental Engineering, May 27-30, Vienna, Austria. (Accepted as Oral presentation)
• Katipoglu-Yazan, T., Dev, S., Desmond-Le Quéméner, E., Bouchez, T., (2021). What is the link between T, µmax and dissipation as heat during microbial growth? 16^ème Congrès National de la Société Française de Microbiologie, 22-24 Sep, Nantes, France. (Poster Presentation).
• Katipoglu-Yazan, T., Delattre, H., Bouchez, T., Filali, A., (2021). Comparison of conventional and new energy-based models for modeling activated sludge dynamics. 16^ème Congrès National de la Société Française de Microbiologie, 22-24 Sep, Nantes, France. (Oral Presentation).
• Dev, S., Katipoglu-Yazan, T., Desmond-Le Quéméner, E., Bouchez, T., (2021). Non-equilibrium physical principles explain the temperature dependency of microbial growth: theory and experiments. 16^ème Congrès National de la Société Française de Microbiologie, 22-24 Sep, Nantes, France. (Oral Presentation).

Nitrification Process Modeling

• Katipoglu-Yazan, T., Ubay-Cokgor, E., Orhon, D. Kinetic Responses of Enriched Nitrifying Systems to Acute Erythromycin and Tetracycline Exposure. (Under Review) Environmental Technology.
• Leblebici, B., Insel, G., Güven, D., Katipoglu-Yazan, T., Cokgor, E. Uncertainty Analysis in the Measurement of Nitrification Kinetics in Urban Wastewater Treatment Plants. (Under Review) Environmental Technology.
• Katipoglu-Yazan, T., Ubay-Cokgor, E., Orhon, D., (2025). Acute impact of SMX, TET, and ERY on enriched nitrifying system kinetics: a comparison with mixed microbial culture. IWA-International Symposium on Waste Management Problems in Agro-Industries, September 10-12, Istanbul, Turkiye. (Oral Presentation)
• Katipoglu‐Yazan, T., Ubay‐Cokgor, E., Orhon, D., (2023) Significance of enriched culture on the assessment of the acute inhibitory impact of sulfamethoxazole on nitrifying biomass. J. Chem. Technol. Biot. 98(3): 706-717. 
• Katipoglu-Yazan, T., Ubay-Cokgor, E, Orhon, D.,(2021). Acute inhibitory impact of sulfamethoxazole on mixed microbial culture: Kinetic analysis of substrate utilization biopolymer storage nitrification and endogenous respiration. Biochemical Eng. J, 167, 107911. 
• Katipoglu-Yazan, T., Ubay-Cokgor, E, Orhon, D.,(2018).Chronic impact of sulfamethoxazole: How does process kinetics relate to metabolic activity and composition of enriched nitrifying microbial culture?. J. Chem. Technol. Biot. 93(6): 1722-1732. 
• Katipoglu-Yazan, T., Merlin,C., Pons,M.N., Ubay-Cokgor,E., Orhon,D., (2016). Chronic impact of sulfamethoxazole on the metabolic activity and composition of enriched nitrifying microbial culture. Water Res. 100: 546–555. 
• Katipoglu-Yazan, T., Merlin,C., Pons,M.N., Ubay-Cokgor,E., Orhon,D., (2015). Chronic impact of tetracycline on nitrification kinetics and the activity of enriched nitrifying microbial culture. Water Res. 72: 227-238. 
• Katipoglu-Yazan, T., Pala-Ozkok, I., Ubay Cokgor, E., Orhon, D., (2014). Acute impact of tetracycline and erythromycin on the storage mechanism of polyhydroxyalkanoates. Biochem. Eng. J. 91: 283-289. 
• Katipoglu-Yazan, T., Pala-Ozkok, İ., Ubay Cokgor, E., Orhon, D., (2013a) Acute impact of erythromycin and tetracycline on the kinetics of nitrification and organic carbon removal in mixed microbial culture. Bioresour. Technol. 144, 410-419. 
• Katipoglu-Yazan, T., Ubay Cokgor, E., Orhon, D. (2013) Modeling sequential ammonia oxidation kinetics in enriched nitrifying microbial culture. J. Chem. Technol. Biot. 90:72-79.

Activated Sludge Modeling

• Pala-Ozkok, I., Katipoglu-Yazan, T., (2024). Editorial: Antibiotics in engineered and natural environments: occurrence, fate, kinetic and microbial impact. Frontiers in Antibiotics. Sec. Antibiotic Resistance, 3, 1437802. 
• Pala-Ozkok, I., Katipoglu-Yazan, T., Olmez-Hanci, T., Jonas, D., Ubay-Cokgor, E., Orhon, D., (2024). Impact of acute and chronic exposure to sulfamethoxazole on the kinetics and microbial structure of an activated sludge community. Frontiers in Antibiotics. Sec. Antibiotic Resistance, 3, 1335654. 
• Katipoglu-Yazan, T., (2015).Modeling aerobic stabilization of domestic and industrial sludge using a multi-component biomass model. Environ. Technol. 36: 2013-2023. 
• Pala-Ozkok, P., Katipoglu-Yazan, T., Ubay-Cokgor, E., Insel, G., Orhon, D., (2011). Respirometric assessment of substrate binding by antibiotics in peptone biodegradation. J. Env. Sci. & Healt. Part A 46(13): 1588-97.
• Cokgor, E.U., Insel, G., Katipoglu, T., Orhon, D., (2011). Biodegradation kinetics of peptone and 2,6-dihydrobenzoic acid by acclimated dual microbial culture. Bioresour. Technol. 102(2): 567-575. 
• Katipoglu, T., Cokgor, E.U., Insel, G., Orhon, D., (2010). Biodegradation kinetics of 2,6-dihydroxybenzoic acid and peptone mixture by acclimated microbial culture at low sludge age. J. Env. Sci. & Healt. Part A 45(14): 1885–1891.
• Katipoglu, T., Cokgor, E.U., Insel, G., Orhon, D., (2010). Response of mixed microbial culture to 2,6-dihydroxybenzoic acid and peptone mixture at low sludge age-effect of culture history. J. Env. Sci. & Healt. Part A 45(7): 875–882.
• Orhon, D., Ubay Cokgor, E., Katipoglu, T., Insel, G., Karahan, O.,(2010). Fate of 2,6-dihydroxybenzoic acid and its inhibitory impact on the biodegradation of peptone under aerobic conditions. Bioresour. Technol. 101(8): 2665-2671.
• Orhon, D., Ubay Cokgor, E., Insel, G., Karahan, O., Katipoglu, T., (2009). Validity of Monod kinetics at different sludge ages – Peptone biodegradation under aerobic conditions. Bioresour. Technol., 100, 5678-5686. 
• Insel, G., Karahan, O., Ozdemir, S., Pala, I., Katipoglu, T., Cokgor, EU., Orhon, D., (2006).Unified basis for the respirometric evaluation of inhibition for activated sludge. J Sci & Health–Part A 41(9): 1763–1780. 

RELATED PROJECTS

• (2026-) Metagenomic and metatranscriptomic analysis of nitrification communities under chronic pollutant exposure and model calibration using the microbial transition state approach. General Research Project, Istanbul Technical University-Turkiye. 

• (2016-2021) Agence Nationale de la Recherche-Funded Projects: A THERMOdynamic framework for modelling MICrobial growth and community dynamics  – Thermomic, France.

RELATED DOCTORAL STUDIES

• Soylu, D., “Modeling of Chronic Inhibition Effects of Selected Pollutants on Nitrification Using Microbial Transition State Theory” Istanbul Technical University. (Ongoing, Supervisors: Tuğçe Katipoğlu Yazan and Emine Ubay Çokgör).