Assoc. Prof. Štěpán Papáček, Ph.D.

research fellow

Štěpán Papáček
papacek@utia.cas.cz 266052392 Personal web
Department: Department of Control Theory
Research interests: Mathematical modeling, control, and Design of Experiments (DoE) of biological processes, such as Integrated Multi-Trophic Aquaculture (IMTA) systems and photosynthesis in macro and microalgal mass cultures, e.g., photobioreactors (PBRs). Advanced computational tools are used for modeling, simulations, and eventually optimization of these systems, including computational fluid dynamics (CFD), as well as techniques for solving inverse problems of model parameter identification.

Biography

Publication list

Stepán Papácek graduated from the Faculty of Mechanical Engineering, Czech Technical University in Prague, in 1986. He received his Ph.D. from the Faculty of Mechatronics and Interdisciplinary Engineering Studies at the Technical University of Liberec, Czech Republic, in 2005.

From 1994 to 2000, he held the position of Ordinarius Professor in various subjects—including Mechanics, Machine Design, Robotics, and Control Theory—at Universidad Panamericana, Guadalajara, Mexico, and at CINVESTAV-IPN, Unidad Guadalajara, in 1999. From 2000 to 2019, he was per partes a researcher and lecturer at the Institute of Physical Biology, University of South Bohemia in Nové Hrady, Czech Republic.

In 2020, he completed his habilitation at VŠB–Technical University of Ostrava and was awarded the title of Associate Professor. Since 2020, he has been a research fellow in the Department of Control Theory at the Institute of Information Theory and Automation (UTIA), Czech Academy of Sciences, Prague.

His main scientific interests include mathematical modeling of biological systems and processes, with a particular focus on model identification and calibration, which is closely linked to model-based experimental design. His work involves modeling photobioreactors (PBRs), recirculating aquaculture systems (RAS), and integrated multitrophic aquaculture (IMTA) systems using computational fluid dynamics (CFD). Recently, he has returned to his original specialization in modeling and simulation of multibody systems, with a growing interest in bipedal locomotion in both robots and humans.

Books and chapters

  1. Polach P., Papáček Štěpán: ON A STEPLADDER CYCLIC WALKING: STRUCTURE AND PARAMETERS IDENTIFICATION OF AN UNDERACTUATED HYBRID STATE MODEL, Projektowanie, badania i eksploatacja - 2023 : Monografia, p. 93-100 Download DOI: 10.53052/9788367652148 [2023]

Journal articles

  1. Filip R., Masaló I., Papáček Štěpán: Modeling and CFD Simulation of Macroalgae Motion within Aerated Tanks: Assessment of Light-Dark Cycle Period, Energies 17 Download Download DOI: 10.3390/en17143555 [2024]
  2. Inostroza C., Papáček Štěpán, Fernández-Sevilla J.M., Acién F. G.: Optimization of thin-layer photobioreactors for the production of microalgae by integrating fluid-dynamic and photosynthesis rate aspects, Journal of Applied Phycology 35 5 (2023), p. 2111-2123 Download DOI: 10.1007/s10811-023-03050-8 [2023]
  3. Matonoha Ctirad, Papáček Štěpán, Lynnyk Volodymyr: On an optimal setting of delays for the D-QSSA model reduction method applied to a class of chemical reaction networks, Applications of Mathematics 67, p. 831-857 Download DOI: 10.21136/AM.2022.0136-21 [2022]
  4. Lynnyk Volodymyr, Papáček Štěpán, Rehák Branislav: Biochemical network of drug-induced enzyme production: Parameter estimation based on the periodic dosing response measurement, Kybernetika 57 6 (2021), p. 1005-1018 Download Download DOI: 10.14736/kyb-2021-6-1005 [2021]
  5. Petera K., Papáček Štěpán, González C.I., Fernández-Sevilla J.M., Fernández F.G.A.: Advanced Computational Fluid Dynamics Study of the Dissolved Oxygen Concentration within a Thin-Layer Cascade Reactor for Microalgae Cultivation, Energies 14 Download Download DOI: 10.3390/en14217284 [2021]

Other publications

  1. Papáček Štěpán, Matonoha Ctirad: A note on the OD-QSSA and Bohl-Marek methods applied to a class of mathematical models, Programs and Algorithms of Numerical Mathematics 22 : Proceedings of Seminar, p. 127-136, Eds: Chleboun J., Papež J., Segeth K., Šístek J., Vejchodský T. Download DOI: 10.21136/panm.2024.12 [2025]
  2. Polach P., Prokýšek R., Papáček Štěpán: On underactuated bipedal systems walking: Gait pattern modeling and analysis of a stepladder with decorator, PROCEEDINGS OF COMPUTATIONAL MECHANICS 2024, p. 141-144, Eds: Adámek V., Jonášová A., Plánička S. Download Download [2024]
  3. Papáček Štěpán, Matonoha Ctirad: A note on the D-QSSA method with optimal constant delays applied to a class of mathematical models, PANM 22: Programy a algoritmy numericke matematiky 22. Abstrakty, p. 12-12 Download [2024]
  4. Polach P., Prokýšek R., Papáček Štěpán: On a stepladder model walking (with and without a decorator), PROCEEDINGS OF COMPUTATIONAL MECHANICS 2023, p. 167-169, Eds: Adámek Vítězslav, Jonášová Alena, Plánička Stanislav Download [2023]
  5. Papáček Štěpán, Matonoha Ctirad, Sanchez A.: On the D-QSSA Method With Optimal Constant Delays Applied to a Class of Mathematical Models, ODAM 2023 Book of Abstracts, p. 58-58 Download [2023]
  6. Matonoha Ctirad, Papáček Štěpán: Bohl-Marek Formulation of the Nonlinear System of ODEs for a Class of Mathematical Models With Conservation Laws, ODAM 2023 Book of Abstracts, p. 51-52 Download [2023]
  7. Polach P., Anderle Milan, Zezula Pavel, Papáček Štěpán: COMPUTER SIMULATION STUDY OF THE STABILITY OF UNDERACTUATED BIPEDAL ROBOT MODELS (motivated by Griffin and Grizzle, 2017), ENGINEERING MECHANICS 2023 : 29th INTERNATIONAL CONFERENCE - BOOK OF FULL TEXTS, p. 207-210, Eds: Radolf V., Zolotarev I. Download [2023]
  8. Duintjer Tebbens Jurjen, Lanzendörfer M., Matonoha Ctirad, Papáček Štěpán: Preconditioning for the integration of a spatiotemporal pharmacodynamic system, Proceedings in Applied Mathematics and Mechanics, Eds: Böhm Ch., Mang K., Markert B., Reese S., Schmidtchen M., Waimann J., Kaliske M. Download DOI: 10.1002/pamm.202200268 [2023]
  9. Papáček Štěpán, Matonoha Ctirad, Duintjer Tebbens Jurjen: Bohl-Marek decomposition applied to a class of biochemical networks with conservation properties, Proceedings of the Seminar on Numerical Analysis & Winter School /SNA' 23/, p. 56-59, Eds: Starý Jiří, Sysala Stanislav, Sysalová Dagmar Download [2023]
  10. Papáček Štěpán, Matonoha Ctirad: An enhanced model parameter estimation by a slow-fast decomposition based on the first order two time-scale expansion, Proceedings of the PANM 21 Programy a algoritmy numericke matematiky 21 /2022/, p. 19-19 Download [2023]
  11. Papáček Štěpán, Matonoha Ctirad: TESTING THE METHOD OF MULTIPLE SCALES AND THE AVERAGING PRINCIPLE FOR MODEL PARAMETER ESTIMATION OF QUASIPERIODIC TWO TIME-SCALE MODELS, Programs and Algorithms of Numerical Mathematics 21 : Proceedings of Seminar, p. 163-172, Eds: Kůs P., Papež J., Rozložník M., Segeth K., Šístek J. Download DOI: 10.21136/panm.2022.15 [2023]
  12. Polach P., Anderle Milan, Papáček Štěpán: ON THE DESIGN AND MODELING OF A TRAINER FOR THE UNDERACTUATED WALKING ROBOT WITHOUT ANKLES, Proceedings of 27/28th INTERNATIONAL CONFERENCE (2022), p. 309-312 Download DOI: 10.21495/51-2-309 [2022]
  13. Papáček Štěpán, Polach P., Prokýšek R., Anderle Milan: On a class of biped underactuated robot models with upper body: Sensitivity analysis of the walking performance, Proceedings of the 37th conference on COMPUTATIONAL MECHANICS 2022 (CM 2022), p. 99-102 Download [2022]
  14. Papáček Štěpán, Rehák Branislav, Lynnyk Volodymyr, Lynnyk Anna: Analysis of a Model Reduction Method (D-QSSA) applied to a Class of Biochemical Networks, IFAC-PapersOnLine.Volume 54, Issue 15 - 11th IFAC Symposium on Biological and Medical Systems BMS 2021, p. 568-573 Download DOI: 10.1016/j.ifacol.2021.10.317 [2021]
  15. Papáček Štěpán, Lynnyk Volodymyr: Quasi-steady state assumption vs. delayed quasi-steady state assumption: Model reduction tools for biochemical processes, Proceedings of the 2021 23rd International Conference on Process Control (PC), p. 278-283, Eds: Paulen R., Fikar M. DOI: 10.1109/PC52310.2021.9447532 [2021]
  16. Papáček Štěpán, Lynnyk Volodymyr, Rehák Branislav: REGULATORY NETWORK OF DRUG-INDUCED ENZYME PRODUCTION: PARAMETER ESTIMATION BASED ON THE PERIODIC DOSING RESPONSE MEASUREMENT, Programs and Algorithms of Numerical Mathematics. Proceedings of Seminar, p. 89-97, Eds: Chleboun J., Kůs P., Přikryl P., Rozložník M., Segeth K., Šístek J. Download DOI: 10.21136/panm.2020.09 [2021]
  17. Papáček Štěpán, Matonoha Ctirad, Duintjer Tebbens Jurjen: Mathematics and Optimal control theory meet Pharmacy: Towards application of special techniques in modeling, control and optimization of biochemical networks, Proceedings of the SNA'21 Seminar on Numerical Analysis Modelling and Simulation of Challenging Engineering Problems, p. 60-63, Eds: Starý Jiří, Sysala Stanislav Download [2021]
  18. Papáček Štěpán, Lynnyk Volodymyr, Rehák Branislav: Systems biology analysis of a drug metabolism (with slow-fast. . . ), Proceedings of the PANM 20 Programy a algoritmy numericke matematiky 20 Download [2020]
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