Publications

Preprints

  • M. Ondrušová, I.Cimrák, Dynamical properties of red blood cell model in shear flow, in review process for IDT 2017, 5. - 7. 7. 2017, Žilina, Slovakia, preprint version
  • M. Slavík, K. Bachratá, H. Bachratý, K. Kovalčíková, The Sensitivity of the Statistical Characteristics to the Selected Parameters of the Simulation Model in the Red Blood Cell Flow Simulations, in acceptance process for IDT 2017, 5. - 7. 7. 2017, Žilina, Slovakia, preprint version
  • H. Bachratý, K. Kovalčíková, K. Bachratá, M. Slavík, Methods of exploring the Red Blood Cells rotation during the simulations in devices with periodic topology, in acceptance process for IDT 2017, 5. - 7. 7. 2017, Žilina, Slovakia, preprint version
  • M. Gusenbauer, R. Tóthová, G. Mazza, M. Brandl, T. Schrefl, I. Jančigová, I. CimrákCell damage index as computational model for hemolysis estimation 

 

WoS and Current Contents

  • M. Bušík, I. Jančigová, R. Tóthová, I. Cimrák, Simulation study of rare cell trajectories and capture rate in periodic obstacle arrays, Journal of Computational Science, doi: 10.1016/j.jocs.2016.04.009, online, preprint version.
  • I.Cimrák, Collision rates for rare cell capture in periodic obstacle arrays strongly depend on density of cell suspension, Computer Methods in Biomechanics and Biomedical Engineering, Vol. 19, Iss. 14, pp. 1525-1530, 2016, DOI:10.1080/10255842.2016.1165806, online, local copy.
  • I. Jančigová, I. Cimrák, Non-uniform force allocation for area preservation in spring network models, International Journal for Numerical Methods in Biomedical Engineering, doi: 10.1002/cnm.2757, online, local copy.
  • I. Cimrák, M. Gusenbauer, I. Jančigová, An ESPResSo implementation of elastic objects immersed in a fluid, Computer Physics Communications, Volume 185, Issue 3, March 2014, Pages 900-907, ISSN 0010-4655, online
  • I. Cimrák, M. Gusenbauer, T. Schrefl, Modelling and simulation of processes in microfluidic devices for biomedical applications, Computers and Mathematics with Applications, Vol 64(3), pp. 278-288, 2012. Doi:10.1016/j.camwa.2012.01.062, online.

 

IEEE, AIP and Scopus       

  • M. Gusenbauer, G. Mazza, M. Brandl, T. Schrefl, R. Tóthová, I. Jančigová, I. Cimrák, Sensing platform for computational and experimental analysis of blood cell mechanical stress and activation in microfludics, In Procedia Engineering: Proceedings of the 30th anniversary Eurosensors Conference, September 2016, Budapest, Hungary, Vol. 168, doi:10.1016/j.proeng.2016.11.388, online.
  • M. Bušík, M. Kotus and M. Slavík, Data management system for computational experiments in blood cell modelling: Mesh analysis showcase, 2016 ELEKTRO, Strbske Pleso, 2016, pp. 495-499, doi: 10.1109/ELEKTRO.2016.7512125, online.
  • M. Figurová, D. Pudis, P. Gaso and I. Cimrak, PDMS microfluidic structures for LOC applications, 2016 ELEKTRO, Strbske Pleso, 2016, pp. 608-611, doi: 10.1109/ELEKTRO.2016.7512150. online.
  • I. Cimrák, K. Bachratá, H. Bachratý, I. Jančigová, R. Tóthová, M. Bušík, M. Slavík M. Gusenbauer, Object-in-fluid framework in modeling of blood flow in microfluidic channels, Comunications, Scientific Letters of the University of Zilina, vol. 18/1a, pp. 13-20, 2016, online, local copy.
  • I. Cimrák, I. Jančigová, R. Tóthová, M. Gusenbauer, Mesh-based modeling of individual cells and their dynamics in biological fluids, In: Applications of Computational Intelligence in Biomedical Technology, Vol. 606 of Studies in Computational Intelligence, Springer International Publishing, 2015, ISBN 978-3-319-19146-1, online, preprint version.
  • R. Tóthová, I. Jančigová, M. Bušík, Calibration of elastic coefficients for spring-network model of red blood cell in Information and Digital Technologies (IDT) 2015, International Conference, IEEE, July 2015, Slovakia, ISBN 978-1-4673-7185-8, pp. 376-380, online
  • I. Cimrák, A simplified model for dynamics of cell rolling and cell-surface adhesion, In: AIP Conference Proceedings, 2015, Vol. 1648, eid: 210005, ISBN 978-0-7354-1287-3, online
  • I. Jančigová, I. Cimrák, A novel approach with non-uniform force allocation for area preservation in spring network models,  In: AIP Conference Proceedings, 2015, Vol. 1648, eid: 210004, ISBN 978-0-7354-1287-3, online
  • R. Tóthová I. Cimrák, Local stress analysis of red blood cells in shear flow,  In: AIP Conference Proceedings, 2015, Vol. 1648, eid: 210003, ISBN 978-0-7354-1287-3, online
  • K. Bachratá, H. Bachratý, On modeling blood flow in microfluidic devices in ELEKTRO 2014: 10th International Conference, IEEE, May 2014, Slovakia, ISBN 978-4799-3720-2, pp. 518-521, online.
  • I. Jančigová, R. Tóthová, Scalability of forces in mesh-based models of elastic objects in ELEKTRO 2014: 10th International Conference, IEEE, May 2014, Slovakia, ISBN 978-4799-3720-2, pp. 562-566, online
  • R. Tóthová, I. Jančigová, I. Cimrák, Energy contributions of different elastic moduli in mesh-based modeling of deformable objects,  in ELEKTRO 2014: 10th International Conference, IEEE, May 2014, Slovakia, ISBN 978-4799-3720-2, pp. 534-538, online
  • I. Cimrák, I. Jančigová, R. Tóthová, Recent advances in mesh-based modeling of individual cell in biological fluids in Digital Technologies (DT) 2014: 10th International Conference, IEEE, July 2014, Slovakia, ISBN 978-1-4799-3303-7, pp. 25-31, online

 

Other articles  

  • M. Bušík, I. Cimrák,The calibration of fluid-object interaction in immersed boundary methodEPJ Web of Conferences, Vol. 143, art. no. 02013, 2017, online
  • K. Bachratá, H. Bachratý, M. Slavík, Statistics for comparison of simulations and experiments of flow of blood cells, EPJ Web of Conferences, Vol. 143, art. no. 02002, 2017, online
  • M. Gusenbauer, G. Mazza, M. Brandl, T. Schrefl, R. Tóthová, I. Jančigová, I. Cimrák, Cell  rheology in microfluidic perfusion: computational and experimental approach, In 42nd International Conference on Micro and Nano Engineering, 2016, preprint version
  • I. Cimrák, K. Kovalčíková, Single cell modelling in microfluidics and in design of cell sorting and cell manipulation devices, In: Micro and Nanoscale Technologies for the Life Sciences, 2016, NanoBioTech conference, 7-9 November 2016, Montreux, Switzerland, preprint version
  • K. Kovalčíková, K. Bachratá, H. Bachratý, M. Slavík, Study on sensibility of statistical characteristics of flow of elastic objects in fluid, In: Micro and Nanoscale Technologies for the Life Sciences, 2016, NanoBioTech conference, 7-9 November 2016, Montreux, Switzerland, preprint version
  • M. Bušík, The analysis of fluid discretization and its impact on elastic object immersed in fluid, In: MiST 2016 Mathematics in Science and Technologies: proceedings of the MiST conference 2016, Fačkovské sedlo, Kľak, Slovakia, January 2-7, 2016. University of Žilina, 2016. ISBN 978-1533605665, preprint version
  • I. Jančigová, A comparison of two computational models for simulations of red blood cells in flow, In: MiST 2015 Mathematics in Science and Technologies: proceedings of the MiST conference 2015, Fačkovské sedlo, Kľak, Slovakia, January 19-24, 2015. University of Žilina, 2015. ISBN 978-1514866382, preprint version
  • R. Tóthová, Method of calibration of red blood cell model by stretching experiments, In: MiST 2015 Mathematics in Science and Technologies: proceedings of the MiST conference 2015 Fačkovské sedlo, Kľak, Slovakia, January 19-24, 2015. University of Žilina, 2015. - ISBN 978-1514866382, preprint version
  • M. Bušík, Viscoelasticity in spring network models for proper dynamics of cell membrane, Journal of Information, Control and Management Systems, [S.I.], v. 13, n. 1, apr. 2015. ISSN 1336-1716, online
  • I. Jančigová, On mass distribution in Espresso In: MiST 2014 Mathematics in Science and Technologies: proceedings of the MiST conference 2014 Fačkovské sedlo, Kľak, Slovakia, January 3-8, 2014. University of Žilina, 2014. - ISBN 978-1500136413, preprint version
  • R. Tóthová, Comparison of Different Formulas for Local Area Conservation Modulus in Spring Network Models In: MiST 2014 Mathematics in Science and Technologies: proceedings of the MiST conference 2014 Fačkovské sedlo, Kľak, Slovakia, January 3-8, 2014. University of Žilina, 2014. - ISBN 978-1500136413, preprint version
  • I. Jančigová, Lattice-Boltzmann method used to model elastic objects in fluid. In: MiST 2013 Mathematics in Science and Technologies: proceedings of the MiST conference 2013 : Fačkovské sedlo, Kľak, Slovakia, January 7-12, 2013. - Žilina: University of Žilina, 2013, ISBN 978-80-554-0730-2, preprint version
  • R. Tóthová (in Slovak language only), Modelovanie pohybu červených krviniek v mikrofluidických zariadeniach. In: 8th Workshop on Intelligent and Knowledge oriented Technologies: November 21-22, 2013 Herľany, Slovakia: proceedings. - Košice: Centre for Information Technologies, Faculty of Electrical Engineering and Informatics, Technical University in Košice, 2013. - ISBN 978-80-8143-128-9. - S. 99-103, preprint version
  • I. Cimrák, I. Jančigová, K. Bachratá, H. Bachratý, On elasticity of spring network models used in blood flow simulations in ESPResSo. In: Particle-Based Methods III : fundamentals and applications : 18-20 September 2013, Stuttgart, Germany. - Barcelona: International center for numerical methods in engineering (CIMNE), 2013. - ISBN 978-84-941531-7-4. - pp. 133-144, online
  • M. Gusenbauer, I. Cimrák, S. Bance, L. Exl, F. Reichel, H. Oezelt, T. Schrefl, A tunable cancer cell filter using magnetic beads: cellular and fluid dynamic simulations, preprint version. This work was highlighted by the MIT Technology Review in its article How to Spot Circulating Tumor Cells.

 

In case you can not obtain our manuscripts via your institution, please contact us at ivan.cimrak@fri.uniza.sk. We will send you a copy.

events&news

04.04. 2017
New PhD positions

In our research group we open two PhD positions starting from September 2017. More information are available at dedicated page.

10.01. 2017
Invitation to a Workshop

Cell-in-fluid Research Group organizes the 2nd Workshop on Modelling of Biological Cells, Fluid Flow and Microfluidics - February 5-9, 2017. More information here.

10.05. 2016
New article published

The members of our group published an article in Journal of Computational Science (2015 Impact Factor 1.231). The title of the article is Simulation study of rare cell trajectories and capture rate in periodic obstacle arrays. Congratulate Martin, Iva, Renáta and Ivan.

08.04. 2016
New article published

Recently, new article has been published in Computer Methods in Biomechanics and Biomedical Engineering,  (Impact Factor 1.770). The title of the article is Collision rates for rare cell capture in periodic obstacle arrays strongly depend on density of cell suspension. The article is available at journal website or at our publication section

08.01. 2016
New article published

Recently, new article has been published in International Journal for Numerical Methods in Biomedical Engineering (Impact Factor 2.052). The title of the article is Non-uniform force allocation for area preservation in spring network models. The article is available at journal website or at our publication section. Congratulate Iveta and Ivan.

04.09. 2015
Welcome new colleagues

Starting in September, two doctoral students joined the group: Martin Slavik and Marek Kotus. Welcome!

26.08. 2015
PhD degree obtained

We congratulate Iveta on obtaining the PhD degree. Good luck (not only) in your further scientific research.

02.08. 2015
Conference in Edinburg

In July, Iveta and Martin B. attended the Discrete Simulation of Fluid Dynamics (DSFD2015) conference. They presented our preliminary results on analysis of periodic obstacle arrays.

15.10. 2014
ICNAAM

Our group participated at ICNAAM 2014 conference. I.Cimrák organized a symposium at the conference with title Modelling of Biological Cells, Fluid Flow and Microfluidics. 

05.09. 2014
New members in the group

Two new PhD students have joined our research group: Jana Kadlecová and Martina Bušík. Welcome :-)

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