Publikace

2023

Wodecki A., Strachota P., Oberhuber T., Škardová K., Balázsová M., Bohatý M., Numerical optimization of the Dirichlet boundary condition in the phase field model with an application to pure substance solidification, Computers & Mathematics with Applications, vol. 145, no. 1, pp. 90-105, 2023, IF 2.9.

Eichler P., Galabov R., Fučík R., Škardová K., Oberhuber T., Pauš P., Tintěra J., Chabiniok R., Non-Newtonian turbulent flow through aortic phantom: Experimental and computational study using magnetic resonance imaging and lattice Boltzmann method, Computers & Mathematics with Applications, vol. 136, no. 15, pp 80-94, 2023, IF 3.218.

Wodecki A., Balázsová M., Strachota P., Oberhuber T., Existence of Optimal Control for Dirichlet Boundary Optimization in a Phase Field Problem, Journal of Dynamical and Control Systems, 2023, IF 1.425

Šístek J., Oberhuber T., Acceleration of a parallel BDDC solver by using graphics processing units on subdomains, The International Journal of High Performance Computing Applications, vol. 37, no.2, pp. 151-164, 2023, IF 2.820.

2022

Galabov R., Škardová K., Chabiniok R., Oberhuber T., Fučík R., Eichler P., Kovář J., Pauš P., Wodecki A., Tintěra J., Zkušenosti s použitím a zpracováním dat z měření průtoků magnetickou rezonancí sekvencí 4D Flow, Česká radiologie, vol. 76 no. 4, pp. 249 -255, 2022.

Fučík R., Eichler P., Klinkovský J., Straka R. Oberhuber T., Lattice Boltzmann Method Analysis Tool (LBMAT), Numerical Algorithms, 2022, IF 3.041.

Klinkovský J., Oberhuber T., Fučík R., Žabka V., Configurable open-source data structure for distributed conforming unstructured homogeneous meshes with GPU support, ACM Transactions on Mathematical Software, vol. 48, no. 3, article no. 3, pp. 1--30, 2022, IF 2.043.

2021
Chabiniok R., Škardová K., Galabov R., Eichler P., Gusseva M., Janoušek J., Fučík R., Tintěra J., Oberhuber T., Hussain T. Translational Cardiovascular Modeling: Tetralogy of Fallot and Modeling of Diseases. In: Málek, J., Süli, E. (eds) Modeling Biomaterials. Nečas Center Series. Birkhäuser, Cham, 2021.

Škardová K., Oberhuber T., Tintěra J., Chabiniok R., Signed-distance function based non-rigid registration of image series with varying image intensity, Discrete and Continuous Dynamical Systems S, vol. 14, no. 3, pp. 1145-1160, 2021, IF 1.233

Oberhuber T., Dytrych T., Launey, K. D., Langr D., Draayer, J.P., Transformation of a Nucleon-Nucleon potential operator into its SU(3) tensor form using GPUs, Discrete and Continuous Dynamical Systems S, vol. 14, no. 3, pp. 1111-1122, 2021, IF 1.233

2020

Pevný T., Šmídl V., Trapp M., Poláček O., Oberhuber T., Sum-Product-Transform Networks: Exploiting Symmetries using Invertible Transformations, Proceedings of the 10th International Conference on Probabilistic Graphical Models, PMLR 138:341-352, 2020.

Oberhuber T., Klinkovský J., Fučík R., TNL: Numerical library for modern parallel architectures, Acta Polytechnica, vol. 61, no. SI, pp. 122-134, 2020.

Eichler P., Malík M., Oberhuber T., Fučík R., Numerical investigation of the discrete solution of phase-field equation, Proceedings of Algoritmy 2020, pp. 111-120, 2020.

Škardová K., Eichler P., Oberhuber T., Fučík R., Investigation of Blood-Like Non-Newtonian Fluid Flow in Stenotic Arteries using the Lattice Boltzmann Method in 2D, Proceedings of Algoritmy 2020, pp. 91-100, 2020.

2019
Knapp F., Dytrych T., Langr D., Oberhuber T., Importance Basis Truncation in the Symmetry-adapted No-core Shell Model,
Acta Physica Polonica B., vol. 50, no. 3, pp. 541--547, 2019, IF 0.904 (0.875).

2018

Fučík R., Klinkovský J., Solovský J., Oberhuber T., Mikyška J., Multidimensional Mixed-Hybrid Finite Element Method for Compositional Two-Phase Flow in Heterogeneous Porous Media and its Parallel Implementation on GPU, Computer Physics Communications, vol. 238, pp. 165-180. IF 3.748 (4.284)

Fučík R., Eichler P., Straka R., Pauš P., Klinkovský J., Oberhuber T., On optimal node spacing for immersed boundary-lattice Boltzmann method in 2D and 3D, Computers and Mathematics with Applications, vol. 77, no. 4, pp. 1144-1162, 2019. IF 1.86 (2.08)

Langr D., Dytrych T., Oberhuber, T., Knapp, F., Efficient Parallel Generation of Many-Nucleon Basis for Large-Scale Ab Initio Nuclear Structure Calculations, Parallel Processing and Applied Mathematics Part II.. Cham: Springer International Publishing AG, 2018. pp. 341-350. Lecture Notes in Computer Science. vol. 10778, 2018.

Knapp F., Dytrych T., Langr D., Oberhuber T., Importance truncation in the SU(3) symmetry-adapted no-core shell model , Acta Physica Polonica B, vol. 11, no. 1, pp. 65--72, 2018. IF 0.904 (0.756).

2017

Hanousek V., Oberhuber T., Efficient transfer of C++ objects on Intel Xeon Phi coprocessor on offload mode, Computer Methods in Material Science, vol. 17, no. 2, pp. 94-100, 2017, PDF.

2016

Klement V., Oberhuber T., Ševčovič D., Application of the level-set model with constraints in image segmentation , Numerical Mathematics: Theory, Methods and Applications, vol. 9, no. 1, pp.147-168, 2016. IF 0.71 (0.83), PDF.

Cited by:

Sourati J., Brooks D.H., Dy J. G., Erdogmus D., Constrained spectral clustering for image segmentation, Machine Learning for Signal Processing (MLSP), 2012 IEEE International Workshop on, pp. 1--6, 2012.

2015

Bauer P., Klement V., Oberhuber T., Žabka V., Implementation of the Vanka-type multigrid solver for the finite element approximation of the Navier-Stokes equations on GPU, Computer Physics Communication, Vol.200, pp.50-56,2016.IF 3.112 (3.508).

Dytrych T., Hayes A. C., Launey K. D., Draayer J. P., Maris P., Vary J. P., Langr D., Oberhuber T., Electron-scattering form factors for 6Li in the ab initio symmetry-guided framework, Physical Review C, 91, 024326, IF 3.881, PDF.

Oberhuber T., Numerical solution for the anisotropic Willmore flow of graphs, Applied Numerical Mathematics, Vol. 88, pp.1--17, 2015. IF 1.036 (1.207), PDF.

Bauer, P., Beneš, M., Fučík, R., Hoang, H. D., Klement, V., Máca, R., Mach, J., Oberhuber, T., Strachota, P., Žabka, V., and Havlena, V. Numerical Simulation of Flow in Fluidized Beds, . Discrete. Cont. Dyn. S. S, issue 8, pages 833--846, 2015 IF 0.567.

Dytrych T., Launey K. D., Draayer J. P., Maris P., Vary J. P., Langr D., Oberhuber T., Emergence of Simple Patterns in Complex Atomic Nuclei from First Principles, Journal of Physics: Conference Series 639, 01200, 2015, IF 0.45.

Klement V., Oberhuber T., Multigrid Method for Linear Complementarity Problem and Its Implementation on GPU, International Journal of Applied Mathematics, Vol. 54, No. 3, 2015.

2014

Oberhuber T., Kučera S., Loucký J., Súkupová L., Tintěra J., Segmenting Tagged Cardiac MRI Data Using a Local Variance Filter, Acta Polytechnica, Vol. 54, No. 3, pp. 214--220,2014, PDF.

2013
Hoang D. H., Beneš M., Oberhuber T., Numerical Simulation of Anisotropic Mean Curvature of Graphs in Relative Geometry, Acta Polytechnica Hungarica,
Vol. 10, No. 7, pp. 99--115, 2013, IF 0.588, PDF.

Cited by:

Pap E., Szakál A., Binary copulas as aggregation functions, 15th IEEE International Symposium on Computational Intelligence and Informatics, pp. 369-372, 2014.
Ševčovič D., Trnovská M., Solution to the inverse Wulff problem by means of the enhanced semidefinite relaxation method, Journal of Inverse and Ill-posed Problems, (WoS citation)

2012

Handlovičová A., Mikula K., Oberhuber T., Comparison of finite volume schemes for the mean curvature flow level set equation, RIMS Kokyuroku Bessatsu, B35, pp. 9 -- 22, 2012, PDF.

Beneš M., Oberhuber T., Strachota P., Straka R., Havlena V., Mathematical modelling of combustion and biofuel co-firing in industrial steam generators, RIMS Kokyuroku Bessatsu, B35, pp. 9 -- 22, 2012.

Fabian D., Mařík R., Oberhuber T., Towards a Formalism of Configuration Properties Propagation, Proceedings of the Workshop on Configuration at ECAI 2012, 2012, Mayer W. and Albert P. (ed), pages 15-20, PDF

Heller M., Oberhuber T., Improved Row-grouped CSR Format for Storing of Sparse Matrices on GPU, Proceedings of Algoritmy 2012, 2012, Handlovičová A., Minarechová Z. and Ševčovič D. (ed.), pages 282-290, ISBN 978-80-227-3742-5, PDF

Cited by:

D. Langr, P. Tvrdík, Evaluation Criteria for Sparse Matrix Storage Formats, IEEE Transactions on parallel and distributed systems,
Oyarzuna G., Borrellb R., Gorobetsa A., Oliva A., MPI-CUDA sparse matrix–vector multiplication for the conjugate gradient method with an approximate inverse preconditioner, Computers and Fluids, vol. 20, pp. 244-252, 2014. (WoS citation)
Maggioni M., Berger-Wolf T., AdELL: An Adaptive Warp-Balancing ELL Format for Efficient Sparse Matrix-Vector Multiplication on GPUs, 42nd International Conference on Parallel Processing (ICPP), pp. 11--20, 2013.(WoS citation)

Loucký J., Oberhuber T., Graph cuts in segmentation of a left ventricle from MRI data, Proceedings of Czech-Japanese Seminar in Applied Mathematics 2010, editors Beneš M., Kimura M., Yazaki S., COE Lecture Note, 2012, vol. 36, pp 46-54, ISSN 1881-4042, PDF, BIB.

Cited by:

Máca R., Beneš M., Application of a degenerate diffusion method in 3D medical image processing, Proceedings of Algoritmy 2012, 2012, Handlovičová A., Minarechová Z. and Ševčovič D. (ed.), pp. 416--426 , 2012. (WoS citation)

2011
Oberhuber T., Suzuki A., Vacata J., New Row-grouped CSR format for storing the sparse matrices on GPU with implementation in CUDA, Acta Technica, 2011, vol. 56, no. 4, pp. 447-466, PDF, BIB.

Cited by:

J. L. Greathouse, M.Daga, Efficient sparse matrix-vector multiplication on GPUs using the CSR storage format, Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, pp. 769-780, 2014. (WoS citation)
X. Guo, X. Liu, P. Xu, Z. Du, E. Chow, Efficient Particle-Mesh Spreading on GPUs, Procedia Computer Science, vol. 51, pp. 120-129, 2015.
Cheik A. A. K., Magoules F., Accelerated Solution of Helmholtz Equation with Iterative Krylov Methods on GPU, High Performance Computing and Communications, 2014 IEEE 6th Intl Symp on Cyberspace Safety and Security, pp. 54-61, 2014.
D. Langr, P. Tvrdík, Evaluation Criteria for Sparse Matrix Storage Formats, IEEE Transactions on parallel and distributed systems,
W. Yang, K. Li, Z. Mo, K. Li, Performance Optimization Using Partitioned SpMV on GPUs and Multicore CPUs , IEEE Transaction on Computers, 2014. (WoS citation)
F. Magoulèsa, A.-K. Ch. Ahameda, and R. Putanowiczb, Auto-tuned Krylov methods on cluster of graphics processing unit, International Journal of Computer Mathematics, vol.92, no. 6, pp. 1222-1250, 2015. (WoS citation)
K. Li, W. Yang, K. Li, Performance Analysis and Optimization for SpMV on GPU Using Probabilistic Modeling, IEEE Transactions on parallel and distributed systems, (WoS citation)
C. Zheng, S. Gu, T.-X. Gu, B. Yang, X.-P. Liu, BiELL: A bisection ELLPACK based storage format for optimizing SpMV on GPUs, J. Parallel Distrib. Comput. 2014.(WoS citation)
Wangdong Y., Keqin L., Performance Analysis and Optimization for SpMV on GPU Using Probabilistic Modeling, IEEE Transactions on Parallel and Distributed Systems, 28 Feb. 2014.(WoS citation)
Oyarzuna G., Borrellb R., Gorobetsa A., Oliva A., MPI-CUDA sparse matrix–vector multiplication for the conjugate gradient method with an approximate inverse preconditioner, Computers and Fluids, vol. 20, pp. 244-252, 2014. (WoS citation)
Li R., Saad Y., GPU-accelerated preconditioned iterative linear solvers, The Journal of Supercomputing, Vol. 63, No. 2, pp. 443-466, 2013.(WoS citation)
Maggioni M., Berger-Wolf T., AdELL: An Adaptive Warp-Balancing ELL Format for Efficient Sparse Matrix-Vector Multiplication on GPUs, 42nd International Conference on Parallel Processing (ICPP), pp. 11--20, 2013.(WoS citation)
Ahamed A.-K. Ch., Magoules F., Iterative Krylov Methods for Gravity Problems on Graphics Processing Unit, Distributed Computing and Applications to Business, Engineering & Science (DCABES), 2013 12th International Symposium on, pp. 16--20, 2013.(WoS citation)
Maggioni M., Berger-Wolf T., An Architecture-Aware Technique for Optimizing Sparse Matrix-Vector Multiplication on GPUs, Procedia Computer Science, vol. 18, pp. 329–338, 2013.(WoS citation)
Ahamed A.-K. C., Magoules F., Fast Sparse Matrix-Vector Multiplication on Graphics Processing Unit for Finite Element Analysis, IEEE 14th International Conference on High Performance Computing and Communications, pp. 1307 - 1314 , 2012. (WoS citation)
Weber D., Bender J., Schnoes M., Stork A., Fellner D., Efficient GPU Data Structures and Methods to Solve Sparse Linear Systems in Dynamics Applications, Computer Graphics Forum, vol. 32 no 1. pp. 16-26 2013. (WoS citation)
Chauhan K., Ashraf J., Accelerating MATLAB Applications on Parallel Hardware, International Journal of Computer Science and Network, vol. 1, no. 4, pp. 80--84, 2012.
Li R., Saad. Y., GPU-accelerated preconditioned iterative linear solvers. Technical Report umsi-2010-112, Minnesota Supercomputer Institute, University of Minnesota, Minneapolis, MN, 2010
Koza Z., Matyka M., Szkoda S., Miroslawb L., Compressed Multiple-Row Storage Format, arxiv.org, http://arxiv.org/abs/1203.2946.

Oberhuber T., Suzuki A., Vacata J., Žabka V., Image segmentation using CUDA implementations of the Runge-Kutta-Merson and GMRES methods, Journal of Math-for-Industry, 2011, vol. 3, pp. 73–79, PDF, BIB.

Cited by:

Al-Ayyoub M. , Abu-Dalo A. M., Jararweh Y., Jarrah M., Al Sa’d M., A GPU-based implementations of the fuzzy C-means algorithms for medical image segmentation, Journal of Supercomputing, 2015. (WoS citation)
Chauhan K., Ashraf J., Accelerating MATLAB Applications on Parallel Hardware, International Journal of Computer Science and Network, vol. 1, no. 4, pp. 80--84, 2012.

Oberhuber T., Suzuki A., Žabka V., The CUDA implementation of the method of lines for the curvature dependent flows, Kybernetika, 2011, vol. 47, num. 2, pages 251--272, IF 0.445 - PDF, BIB.

Cited by:

Máca R., Beneš M., Application of a degenerate diffusion method in 3D medical image processing, Proceedings of Agoritmy 2012, Handlovičová A., Minarechová Z. and Ševčovič D. (ed.), pages 416--426. (WoS citation)

2009
Oberhuber T., Complementary finite volume scheme for the anisotropic surface diffusion flow, Proceedings of Algoritmy 2009, 2009, Handlovičová A., Frolkovič P., Mikula K. and Ševčovič D. (ed.), pages 153-164, ISBN 978-80-227-3032-7, PDF BIB

Cited by:

Máca R., Beneš M., Application of a degenerate diffusion method in 3D medical image processing, Proceedings of Agoritmy 2012, Handlovičová A., Minarechová Z. and Ševčovič D. (ed.), pages 416--426. (WoS citation)

Oberhuber T., Numerical Solution of Willmore Flow, PhD thesis, Department of Mathematics, Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, December 2009, PDF.

Beneš M., Mikula K., Oberhuber T. and Ševčovič D., Comparison study for Level set and Direct Lagrangian methods for computing Willmore flow of closed planar curves, Computing and Visualization in Science, 2009, vol. 12, pages 307-317, DOI 10.1007/s00791-008-0112-2, PDF BIB

Cited by:

Esedoglu S., Ratz A., Roger M., Colliding interfaces in old and new diffuse-interface approximations of Willmore-flow, Commun. Math. Sci., 2014, Vol. 12, No. 1, pp. 125--147.(WoS citation)
Kotorová D., Discrete Duality Finite Volume Scheme for the Curvature-driven Level Set Equation, Acta Polytechnica Hungarica, 2011, Vol. 8, No. 3, pp. 7-12.(WoS citation)
Mikula K., Ševčovič D., Balazovjech M., A Simple, Fast and Stabilized Flowing Finite Volume Method for Solving General Curve Evolution Equations, Commun. Comput. Phys., 2010, Vol. 7, No. 1, pp. 195-211.(WoS citation)
Pauš P., Beneš M., Direct approach to mean-curvature flow with topological changes, Kybernetika Vol. 45, Iss. 4, 2009, pages 591-604. (WoS citation)
Beneš M., Pauš P., Algorithm for topological changes of parametrically described curves, Proceedings of ALGORITMY 2009, 2009, Handlovičová A., Frolkovič P., Mikula K. and Ševčovič, D. (ed.), pp. 176–184. (WoS citation)

2007

Oberhuber T., Finite difference scheme for the Willmore flow of graphs, Kybernetika, vol. 43, 2007, pages 855-867, ISSN 0023-5954, IF 0.293 - PDF BIB

Cited by:

Deckelnick K., Katz J. , Friedhelm Schieweck F. A C1-finite element method for the Willmore flow of two-dimensional graphs, Mathematics og Computation, 2015. (WoS citation)
Pártl O., Computational Studies of Bacterial Colony Model, Scientific Research, Vol. 3, No. 2, 2013, pp. 147-157.
Kimura M., Geometry of hypersurfaces and moving hypersurfaces in Rm for the study of moving boundary problems, Topics in mathematical modeling, Beneš M., Feireisel E., Lecture Notes of Jindřich Nečas for MathematicalModeling, Vol. 4, 2008, pp. 39-94.
Pauš P., Beneš M., Direct approach to mean-curvature flow with topological changes, Kybernetika Vol. 45, Iss. 4, 2009, pages 591-604. (WoS citation)
Strachota P., Implementation of the MR tractography visualisation kit based on the anisotropic Allen-Cahn equation, Kybernetika, Vol. 45, Iss. 4, 2009, pages 657-669. (WoS citation)
Beneš M., Kratochvíl J., Kiristan J., Minárik V. , Pauš P., A parametric simulation method for discrete dislocation dynamics, European Physical Journal, Vol. 177, 2009, pages 177-191. (WoS citation)

Beneš M., Mikula K., Ševčovič D., Oberhuber T., Method of Lines for the Level Set Method for Solving Willmore Flow Geometric Equation, In MAGIA 2007, Slovak University of Technology, Faculty of Civil Engineering, 2007, Vol. 1, pp. 37-44. ISBN 978-80-227-2796-9.

2006

Oberhuber T., Numerical solution for the Willmore flow of graphs, Proceedings of Czech-Japanese Seminar in Applied Mathematics 2006, Beneš M., Kimura M. and Nakaki T. (ed.), Vol. 3, 2005, pages 126-138, ISSN 1881-4042, PDF BIB

Cited by:

Minárik V., Kratochvíl J., Dislocation dynamics – analytical description of the interaction force between dipolar loops, Kybernetika, Vol. 43, No. 6, 2007, pages 841-854.(WoS citation)
Beneš M., Numerical solution for surface diﬀusion on graphs,Proceedings of Czech-Japanese Seminar in Applied Mathematics 2005, Beneš M., Kimura M. and Nakaki T. (ed.), Vol. 3, 2005, pages 9-25, ISSN 1881-4042.
Xu Y., Shu C. W., Local discontinuous Galerkin method for surface diﬀusion and Willmore ﬂow of graphs, Journal of Scientiﬁc Computing, Vo. 40, No. 1-3, 2009, Springer, pp. 375–390. (WoS citation)

2005

Oberhuber T., Computational study of the Willmore flow on graphs, Proceedings of Equadiff-11, Fila M., Handlovičová A., Mikula K., Medved M., Quittner P. and Ševčovič D. (ed.), 2005, pages 321-331, ISBN 978-80-227-2624-5, PDF BIB

2004
Oberhuber T., Numerical recovery of the signed distance function, Proceedings of Czech-Japanese Seminar in Applied Mathematics 2004, Vol. 3, 2004, pages 162-178, ISBN 80-01-03181-0, PDF BIB

Cited by:

Pauš P., Beneš M., Kolář M., Kratochvíl J., Dynamics of dislocations described as evolving curves interacting with obstacles,
Modelling and Simulation in Materials Science and Engineering, vol. 24, no. 3, 035003, 2016.
Kai A. J., Aerostructural Shape and Topology Optimization of Aircraft Wings, PhD thesis, Graduate Department of Institute for Aerospace Studies, University of Toronto, 2012.
Kai A. J., Martins J. R. R. A., An isoparametric approach to level set topology optimization using a body-fitted finite-element mesh, Computers & Structures, 2012, vol. 90-91, pp. 97–106. (WoS citation)
Kai A. J., E. Lee, J. R.R.A. Martins, Stress-based topology optimization using an isoparametric level set method, Finite Elements in Analysis and Design, 2012, vol. 58, pp. 20–30. (WoS citation)

Tomas Oberhuber's Homepage

Navigation

Languages

Syndicate

User login