Research group: Mathematical Modelling Group

Research projects

I participate or participated in and received some funds from the following research projects:

• Off-diagonal thermodynamics and its connection with other factors as a route to predictable selectivity in C-H bond cleavage, project no. GA24-11247S of the Czech Science Foundation (2024-2026).
• Multiphase flow, transport, and structural changes related to water freezing and thawing in the subsurface, project no. 21-09093S of the Czech Science Foundation (2021-2023).
• Development and application of advanced mathematical modeling methods for natural and industrial processes using high-performance computing, project no. SGS20/184/OHK4/3T/14 of the Grant Agency of the Czech Technical University (2020-2022).
• Research centre for informatics, project of excellent research no. CZ.02.1.01/0.0/0.0/16_019/0000765, Operational Programme of Research, Development and Education, Ministry of Education, Youth and Sports of the Czech Republic (2018-2022).
• Computational Models and Experimental Investigation of Fluid Dynamics, Mass Transfer and Transport, and Phase Transitions in Porous Media for Environmental Applications, project Inter-Excelence MSMT no. LTAUSA19021 of Ministry of Education, Youth and Sports of the Czech Republic (2020-2022).
• Analysis of flow character and prediction of evolution in endovascular treated arteries by magnetic resonance imaging coupled with mathematical modeling, project no. NV19-08-00071 of the Ministry of Health of the Czech Republic (2019-2022).
• Research centre for low-carbon energy technologies, project of excellent research no. CZ.02.1.01/0.0/0.0/16_019/0000753, Operational Programme of Research, Development and Education, Ministry of Education, Youth and Sports of the Czech Republic (2018-2022).
• Large structures in boundary layers over complex surfaces under high Reynolds numbers, project no. 18-09539S of the Czech Science Foundation (2018-2020).
• Investigation of shallow subsurface flow with phase transitions, project no. 17-06759S of the Czech Science Foundation (2017-2019).
• Application of advanced supercomputing methods in mathematical modeling of natural processes, project no. SGS17/194/OHK4/3T/14 of the Grant Agency of the Czech Technical University (2017-2019).
• Quantitative mapping of myocard and of flow dynamics by means of MR imaging for patients with nonischemic cardiomyopathy - development of methodology, project no. NV15-27178A of the Ministry of Health of the Czech Republic (2015-2018).
• Advanced supercomputing methods for mathematical modeling of natural processes, project no. SGS14/206/OHK4/3T/14 of the Grant Agency of the Czech Technical University (2014-2016).

Publications

Peer-reviewed articles in impacted journals

• J. Klinkovský, A. C. Trautz, R. Fučík, T. H. Illangasekare, Lattice Boltzmann method–based efficient GPU simulator for vapor transport in the boundary layer over a moist soil: Development and experimental validation.
  Computers & Mathematics with Applications. 2023, 138, 65-87. DOI: 10.1016/j.camwa.2023.02.021
• M. Beneš, P. Eichler, J. Hrdlička, J. Klinkovský, M. Kolář, T. Smejkal, P. Skopec, J. Solovský, P. Strachota, A. Žák, Experimental validation of multiphase particle-in-cell simulations of fluidization in a bubbling fluidized bed combustor.
  Powder Technology. 2023, 416, 118204. ISSN 0032-5910. DOI: 10.1016/j.powtec.2022.118204
• R. Fučík, P. Eichler, J. Klinkovský, R. Straka, T. Oberhuber, Lattice Boltzmann Method Analysis Tool (LBMAT).
  Numerical Algorithms. 2022. ISSN 1572-9265. DOI: 10.1007/s11075-022-01476-8
• J. Klinkovský, T. Oberhuber, R. Fučík, V. Žabka, Configurable open-source data structure for distributed conforming unstructured homogeneous meshes with GPU support.
  ACM Transactions on Mathematical Software. 2022, 48(3), 1-33. ISSN 0098-3500. DOI: 10.1145/3536164
• M. Beneš, P. Eichler, R. Fučík, J. Hrdlička, J. Klinkovský, M. Kolář, T. Smejkal, P. Skopec, J. Solovský, P. Strachota, R. Straka, A. Žák, Experimental and numerical investigation of air flow through the distributor plate in a laboratory-scale model of a bubbling fluidized bed boiler.
  Japan Journal of Industrial and Applied Mathematics. 2022. DOI: 10.1007/s13160-022-00518-x
• T. Oberhuber, J. Klinkovský, R. Fučík, TNL: Numerical library for modern parallel architectures.
  Acta Polytechnica. 2021, 61(SI), 122-134. ISSN 1805-2363. DOI: 10.14311/AP.2021.61.0122
• M. Beneš, P. Eichler, J. Klinkovský, M. Kolář, J. Solovský, P. Strachota, A. Žák, Modeling and Simulation of Bed Dynamics in Oxyfuel Fluidized Bed Boilers.
  Numerical Mathematics and Advanced Applications ENUMATH 2019. Cham: Springer International Publishing AG, 2021. p. 919-927. Lecture Notes in Computational Science and Engineering. vol. 139. DOI: 10.1007/978-3-030-55874-1_91
• M. Beneš, P. Eichler, J. Klinkovský, M. Kolář, J. Solovský, P. Strachota, A. Žák, Numerical simulation of fluidization for application in oxyfuel combustion.
  Discrete and Continuous Dynamical Systems Series – S. 2021, 14(3), 769-783. DOI: 10.3934/dcdss.2020232
• R. Fučík, R. Galabov, P. Pauš, P. Eichler, J. Klinkovský, J. Tintěra, R. Chabiniok, Investigation of phase-contrast magnetic resonance imaging underestimation of turbulent flow through the aortic valve phantom: Experimental and computational study using lattice Boltzmann method.
  Magnetic Resonance Materials in Physics, Biology and Medicine. 2020, 33 649-662. DOI: 10.1007/s10334-020-00837-5
• R. Fučík, P. Eichler, R. Straka, P. Pauš, J. Klinkovský, T. Oberhuber, On optimal node spacing for immersed boundary–lattice Boltzmann method in 2D and 3D.
  Computers & Mathematics with Applications. 2019, 77(4), 1144-1162. DOI: 10.1016/j.camwa.2018.10.045
• R. Fučík, J. Klinkovský, J. Solovský, T. Oberhuber, J. Mikyška, Multidimensional mixed-hybrid finite element method for compositional two-phase flow in heterogeneous porous media and its parallel implementation on GPU.
  Computer Physics Communications. 2019, 238 165-180. DOI: 10.1016/j.cpc.2018.12.004

Contributions in conference proceedings

• M. Beneš, P. Eichler, J. Klinkovský, M. Kolář, T. Smejkal, J. Solovský, P. Strachota, A. Žák, J. Hrdlička, P. Skopec, CFD Simulation and Experimental Analysis of Fluidization in a Model of an Oxyfuel Fluidized Bed Boiler.
  Proceedings of the Conference Algoritmy 2020, Editors: P. Frolkovič, K. Mikula and D. Ševčovič. SPEKTRUM, Slovak University of Technology in Bratislava, 2020, pp. 101-110. ISBN 978-80-227-5032-5. [PDF]

Theses

• J. Klinkovský, Data Structures and Parallel Algorithms for Numerical Solvers in Computational Fluid Dynamics.
  Ph.D. thesis, supervisors T. Oberhuber and R. Fučík, FNSPE, CTU in Prague (2023). [DSpace, PDF, sources]
• J. Klinkovský, Mathematical modelling of two-phase compositional flow in porous media.
  Master‘s thesis, supervisor R. Fučík, FNSPE, CTU in Prague (2017). [PDF]
• J. Klinkovský, Numerical solution of two-phase immiscible flow in porous media with capillarity and its implementation on GPU.
  Research assignment, supervisor R. Fučík, FNSPE, CTU in Prague (2016). [PDF]
• J. Klinkovský, Numerical solution of single-phase flow in porous media and its implementation on GPU.
  Bachelor‘s thesis, supervisor R. Fučík, FNSPE, CTU in Prague (2015). [PDF]

Conferences

2024

• Organizer of the Workshop on Environmental Modeling: Fluid Flow and Transport Phenomena.
  Prague, Czech Republic, 12 June 2024.
• J. Klinkovský, How to simulate passive transport in a turbulent air flow: LBM + LBM or LBM + MHFEM?
  Talk at CFD in Wroclaw, Wroclaw, Poland, 7 June 2024.
• J. Klinkovský, Modern data formats for visualization: Adiós, VTK?
  Talk at Workshop on Scientific Computing, Děčín, Czech Republic, 30 May - 2 June 2024.
• J. Klinkovský, Optimizing LBM for Karolina and LUMI supercomputers.
  Talk at LBM in Kraków, Kraków, Poland, 9 February 2024. [slides]

2023

• J. Klinkovský, Overview of parallel and asynchronous computing in Python.
  Talk at Workshop on Scientific Computing, Děčín, Czech Republic, 25-28 May 2023. [slides]
• J. Klinkovský, A. Trautz, R. Fučík, T. Illangasekare, Development and optimization of a coupled multi-GPU LBM-MHFEM solver for vapor transport in the boundary layer over a moist soil.
  Talk at SIAM Conference on Computational Science and Engineering (CSE23), Amsterdam, The Netherlands, 26 February - 3 March 2023. [slides]
• J. Klinkovský, Optimizing LBM for GPU-accelerated supercomputers.
  Talk at LBM in Kraków, Kraków, Poland, 24 February 2023.
• J. Klinkovský, Simulating bubbling fluidization using Multiphase Particle-in-Cell method in OpenFOAM.
  Talk at Workshop on Applied Mathematics and Scientific Computing, Kanazawa, Japan, 11 January 2023.

2022

• J. Klinkovský, A. Trautz, R. Fučík, T. Illangasekare, Lattice Boltzmann Method–Based GPU Simulator for Vapor Transport in the Boundary Layer Over a Moist Soil.
  Talk at ACOMEN 2022, Liège, Belgium, 31 August - 2 September 2022.
• J. Klinkovský, A. Trautz, R. Fučík, T. Illangasekare, Development and experimental validation of lattice Boltzmann method-based simulator for vapor transport in air over a moist soil layer.
  Talk at InterPore 2022, Abu Dhabi, United Arab Emirates, 30 May - 2 June 2022.
• J. Klinkovský, A. Trautz, R. Fučík, T. Illangasekare, Modeling vapor transport in air using LBM and MHFEM.
  Talk at Workshop on Scientific Computing, Děčín, Czech Republic, 26-29 May 2022.
• J. Klinkovský, A. Trautz, R. Fučík, T. Illangasekare, Development and optimization of a coupled multi-GPU LBM-MHFEM solver for vapor transport in air.
  Talk at HPCSE 2022, Soláň, Czech Republic, 16-19 May 2022.
• J. Klinkovský, M. Beneš, P. Eichler, J. Hrdlička, M. Kolář, T. Smejkal, P. Skopec, J. Solovský, P. Strachota, A. Žák, Multiphase Particle-in-Cell Simulator for Bubbling Fluidized Bed Combustors: Development and Preliminary Results.
  Talk at 18th International Conference on Numerical Combustion, San Diego, California, USA, 8-11 May 2022.
• J. Klinkovský, R. Fučík, A. Trautz, T. Illangasekare, Development and experimental validation of coupled LBM-MHFEM simulator for vapor transport in air over a moist soil layer.
  Talk at LBM in Kraków, Kraków, Poland, 4 February 2022.

2021

• M. Beneš, P. Eichler, J. Klinkovský, M. Kolář, T. Smejkal, J. Solovský, P. Strachota, A. Žák, MP-PIC simulations of fluidization with kotelFoam.
  Talk at Workshop on Scientific Computing, Děčín, Czech Republic, 22-24 August 2021.
• J. Klinkovský, R. Fučík, A. Trautz, T. Illangasekare, Coupled LBM-MHFEM simulator for vapor transport in air over a moist soil layer.
  Poster at InterPore 2021, online, 31 May – 4 June 2021.
• J. Klinkovský, R. Fučík, A. Trautz, T. Illangasekare, Efficient LBM simulator for vapor transport in air over a moist soil layer.
  Talk at LBM in Kraków, online, 5 February 2021.
• J. Klinkovský, R. Fučík, A. Trautz, T. Illangasekare, Efficient LBM simulator for vapor transport in air over a moist soil layer.
  Talk at Czech-Japanese Seminar in Applied Mathematics, online, 5-7 January 2021.

2020

• J. Klinkovský, T. Oberhuber, R. Fučík, TNL: Numerical library for modern parallel architectures and distributed meshes.
  Talk at Workshop on Scientific Computing, online, 4 December 2020.
• P. Eichler, R. Fučík, J. Klinkovský, T. Oberhuber, P. Pauš, R. Straka, A. Wodecki, Optimization of the lattice Boltzmann method for multi-GPU clusters.
  Talk at LBM in Kraków, Kraków, Poland, 7 February 2020.

2019

• J. Klinkovský, R. Fučík, P. Eichler, R. Straka, T. Oberhuber, Performance evaluation of implicit coupling between the immersed boundary and lattice Boltzmann methods on GPU.
  Talk at ICMMES 2019, Edinburgh, United Kingdom, 22-26 July 2019.
• J. Klinkovský, R. Fučík, T. Oberhuber, P. Eichler, R. Straka, Implementation and optimization of an LBM solver for multi-GPU clusters.
  Poster at PUMPS+AI 2019 Summer School, Barcelona, Spain, 24-29 June 2019.
• P. Eichler, R. Fučík, J. Klinkovský, T. Oberhuber, P. Pauš, R. Straka, A. Wodecki, Massively parallel LBM simulations using CUDA and MPI on multiple GPUs.
  Talk at Workshop on Scientific Computing, Děčín, Czech Republic, 30 May - 2 June 2019.
• J. Klinkovský, T. Oberhuber, R. Fučík, Computational study of MGSR- and CWY-based GMRES variants applied to two-phase flow in porous media.
  Talk at HPCSE 2019, Soláň, Czech Republic, 20-23 May 2019.
• J. Klinkovský, T. Oberhuber, R. Fučík, On the scalability of MGSR- and CWY-based GMRES variants for the solver of two-phase flow in porous media using MHFEM discretization.
  Talk at InterPore 2019, Valencia, Spain, 6-10 May 2019.

2018

• J. Klinkovský, R. Fučík, P. Eichler, R. Straka, T. Oberhuber, Numerical simulations of channel flow using lattice Boltzmann method on GPU.
  Talk at Czech–Japanese Seminar in Applied Mathematics, Noto-cho, Japan, 13-16 July 2018.
• J. Klinkovský, V. Žabka, T. Oberhuber, R. Fučík, Statically configurable data structure for conforming unstructured homogeneous meshes on CPUs and GPUs.
  Talk at Workshop on Scientific Computing, Děčín, Czech Republic, 14-17 June 2018.

2017

• J. Klinkovský, R. Fučík, T. Oberhuber, GPU solver for porous media two-phase flow problems using unstructured meshes.
  Poster at GPU Technology Conference, Munich, Germany, 10-12 October 2017.
• J. Klinkovský, NumDwarf: A multidimensional MHFEM/DG numerical scheme for two-phase compositional flow in porous media and its implementation on GPU.
  Talk at CoMFoS17: Mathematical Analysis of Continuum Mechanics, Okinawa Institute of Science and Technology Graduate University (OIST), Japan, 20-22 September 2017.
• J. Klinkovský, R. Fučík, NumDwarf: A general multidimensional MHFEM/DG numerical scheme for solving systems of PDEs on GPU with applications in mathematical modeling of two-phase compositional flow in porous media.
  Talk at Workshop on Scientific Computing, Děčín, Czech Republic, 8-11 June 2017.

2016

• J. Klinkovský, A massively parallel implementation of two-phase immiscible flow in porous media using the mixed-hybrid finite element method.
  Talk at Workshop on Scientific Computing, Děčín, Czech Republic, 9-12 June 2016.

2015

• J. Klinkovský, A massively parallel implementation of mixed hybrid finite element method for single-phase flow in porous media.
  Talk at Workshop on Scientific Computing, Děčín, Czech Republic, 11-14 June 2015.