Marek Piliarik, Ph.D.

Research interests:

Nano-optics; Biophotonics; Microscopy; light scattering; Nanoparticles; Proteins detection, structure and dynamics.

Professional activities:

2016 – dnes: Team leader – Nano Optics, Institute of Photonics and Electronics ASCR, v.v.i.  Prague, Czech Republic
2011 – 2016: Postdoctoral Fellow, Max Planck Institute for the Science of Light and Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
May – July 2011: Postdoctoral Fellow, Swiss Federal Institute of Technology (ETH) in Zürich, Switzerland
2008 – 2011: Postdoctoral Fellow, Institute of Photonics and Electronics ASCR, v.v.i.  Prague, Czech Republic
Sept. 2010: Exchange grant research, Karl-Franzens-University Graz, Institute of Physics, Graz, Austria
2001 – 2002: Visiting Scientist, Electrical Engineering Department, University of Washington, Seattle, USA (11 months)
1998 – 2008: Research Assistant, Institute of Photonics and Electronics ASCR, v.v.i., Prague, Czech Republic (former Institute of Radio Engineering and Electronics)

Education:

2008: Ph.D. in Quantum optics and optoelectronics
Charles University in Prague, Faculty of Mathematics and Physics

2000: MSc. in Optics and optoelectronics
Charles University in Prague, Faculty of Mathematics and Physics

Fellowships and awards:

2015: Fellowship Jana Evangelisty Purkyně
2011: Max-Planck postdoctoral fellowship.
2010: Exchange Grant fellowship, within the framework of the ESF activity PLASMON-BIONANOSENSE

Teaching:

• Contemporary microscopy (NOOE073) - Charles University in Prague, Faculty of Mathematics and Physics

Bibliometrics:

• 5 book chapters
• 45 journal papers
• > 60 conference contributions
• 3 patent (+5 pending)
• > 3200 citations

List of publications

Book chapters:

1. Adam, P., Piliarik, M., Šípová, H., Špringer, T., Vala, M. and Homola, J. Surface Plasmons for Biodetection, in Photonic Sensing: Principles and Applications for Safety and Security Monitoring (eds G. Xiao and W. J. Bock), John Wiley & Sons, Inc., Hoboken, NJ, USA, 2012
2. M. Piliarik, H. Vaisocherová, J. Homola, Surface Plasmon Resonance Biosensing, in Biosensors and Biodetection, Methods and Protocols Volume 1: Optical-Based Detectors, A. Rasooly and K. Herold Editors, Humana Press, 2009, p. 65-88.
3. M. Piliarik, J. Homola, SPR Sensor Instrumentation, in Surface Plasmon Resonance Based Sensors, J. Homola, Editor. Springer-Verlag: Berlin-Heidelberg-New York, 2006, p. 95-116. 
4. J. Homola and M. Piliarik, Surface Plasmon Resonance (SPR) Sensors, in Surface Plasmon Resonance Based Sensors, J. Homola, Editor. Springer-Verlag: Berlin-Heidelberg-New York, 2006, p. 45-67. 
5. J. Štepánek, H. Vaisocherová, M. Piliarik, Molecular Interactions, in Surface Plasmon Resonance Based Sensors, J. Homola, Editor. Springer-Verlag: Berlin-Heidelberg-New York, 2006, p. 69-91. 

Journal papers:

1. Jiří Červenka, Martin Šilhavík, Prabhat Kumar, Zahid Ali Zafar, Martin Míšek, Martin Čičala, Marek Piliarik, Anomalous elasticity and damping in covalently cross-linked graphene aerogels, Commun Phys 5, 27 (2022); doi: https://doi.org/10.1038/s42005-022-00806-5.
2. H. Robert, Ł. Bujak, K. Holanová, M. Vala, V. Henrichs, Z. Lánský, M. Piliarik, Fast photothermal spatial light modulation for quantitative phase imaging at the nanoscale, Nature Communications 12 (2021) 2921
3. M. Vala, M. Piliarik, Weighing single protein complexes on the go, Nature Methods 18 (2021) 1159-1160 (News & Views)
4. M. Vala, L. Bujak, A.G. Marin, K. Holanova, V. Henrichs, M. Braun, Z. Lansky, M. Piliarik, Nanoscopic Structural Fluctuations of Disassembling Microtubules Revealed by Label-Free Super-Resolution Microscopy, Small Methods 5(2021) 2000985
5. Ł. Bujak, K. Holanová, A.G. Marin, V. Henrichs, I. Barvík, M. Braun, Z. Lánský, M. Piliarik, Fast leaps between millisecond confinements govern Ase1 diffusion along microtubules, Small Methods 5 (2021), 2100370
6. Y. He, S. Lin, H. Robert, H. Li, P. Zhang, M. Piliarik, X.-W. Chen, Multiscale Modeling and Analysis for High-fidelity Interferometric Scattering Microscopy, Journal of Physics D: Applied Physics 54 (2021) 274002
7. M. Vala, D. Palounek, H. M. L. Robert, M. Piliarik, Quantitative detection of optical anisotropy of single microtubules by polarization-sensitive interferometric scattering microscopy, Journal of Physics D: Applied Physics 54 (2021) 204001
8. K. Holanová, M. Vala, M. Piliarik, Optical imaging and localization of prospective scattering labels smaller than a single protein, Optics and Laser Technology 109 (2019) 323.
9. M.P. McDonald, A. Gemeinhardt, K. König, M. Piliarik, S. Schaffer, S. Völkl, M. Aigner, A. Mackensen, V. Sandoghdar, Visualizing Single-Cell Secretion Dynamics with Single-Protein Sensitivity, Nano Letters 18 (2018) 513
10. S. Spindler, J. Ehrig, K. Koenig, T. Nowak, M. Piliarik, H. Stein, R. Taylor, E. Garanger, S. Lecommandoux, I. Alves, V. Sandoghdar, Visualization of lipids and proteins at high spatial and temporal resolution via interferometric scattering (iSCAT) microscopy, Journal of Physics D: Applied Physics 49 (2016) 349601.
11. M. Piliarik, V. Sandoghdar: Direct optical sensing of single unlabelled proteins and super-resolution imaging of their binding sites, Nature Communications 5, 2014, 4495
12. M. Piliarik, H. Šípová, P. Kvasnička, N. Galler, J. R. Krenn, J. Homola: High-resolution biosensor based on localized surface plasmons, Optics Express, 20, 2012, 672–680.
13. M. Piliarik, P. Kvasnička, N. Galler, J. R. Krenn, J. Homola: Local refractive index sensitivity of plasmonic nanoparticles, Optics Express 19, 2011, 9213–9220.
14. M. Piliarik, M. Bocková, J. Homola: Surface plasmon resonance biosensor for parallelized detection of protein biomarkers in blood plasma, Biosensors and Bioelectronics 26, 2010, p. 1656–1661. 
15. H. Šípová, M. Piliarik, M. Vala, K. Chadt, P. Adam, M. Bocková, K. Hegnerová, J. Homola: Portable Surface Plasmon Resonance Biosensor for Detection of Nucleic Acids, Procedia Engineering 12, 2011, 148–151
16. M. Vala, K. Chadt, M. Piliarik, J. Homola: High-performance compact SPR sensor for multi-analyte sensing, Sensors and Actuators B 148, 2010, p. 544-549. 
17. F. Fernández, K. Hegnerová, M. Piliarik, F. S. Baeza, J. Homola, M.-Pilar Marco: A label-free and portable multichannel surface plasmon resonance immunosensor for on site analysis of antibiotics in milk samples, Biosensors and Bioelectronics 26, 2010, p. 1231–1238. 
18. T. Špringer, M. Piliarik, J. Homola: Real-time monitoring of biomolecular interactions in blood plasma using a surface plasmon resonance biosensor, Analytical and Bioanalytical Chemistry 398, 2010, p. 1955–1961. 
19. K. Hegnerová, M. Piliarik, M. Šteinbachová, Z. Flegelová, H. Černohorská, J. Homola: Detection of bisphenol A using a novel surface plasmon resonance biosensor, Analytical and Bioanalytical Chemistry 398, 2010, p.1963–1966. 
20. N. D. Brault, C. Gao, H. Xue, M. Piliarik, J Homola, S Jiang, Q. Yu, Ultra-low fouling and functionalizable zwitterionic coatings grafted onto SiO2 via a biomimetic adhesive group for sensing and detection in complex media, Biosensors and Bioelectronics 25, 2010, p. 2276–2282.
21. T. Špringer, M. Piliarik, J. Homola, Surface plasmon resonance with dispersionless microfluidics for direct detection of nucleic acid at the low femtomole level, Sensors and Actuators B-Chemical 145, 2010, p. 588–591.
22. J. Macháček, M.  Piliarik, Věda žije, Chemicke Listy, 104(5), 2021, pp. 301
23. M. Piliarik, J. Homola, Surface plasmon resonance (SPR) sensors: approaching their limits? Optics Express 17(19), 2009, p. 16505–16517.
24. M. Piliarik, M. Vala, I. Tichý, J. Homola: Compact and low-cost biosensor based on novel approach to spectroscopy of surface plasmons, Biosensors and Bioelectronics 24, 2009, p. 3430–3435. 
25. B. Špačková, M. Piliarik, P. Kvasnička, C. Themistos, M. Rajarajan and J. Homola, Novel Concept of Multi-Channel Fiber Optic Surface Plasmon Resonance Sensor, Sensors and Actuators B-Chemical 139(1), 2009, p. 199 – 203.
26. J. Ladd, A. D. Taylor, M. Piliarik, J. Homola, S. Jiang, Label-Free Detection of Cancer Biomarker Candidates Using Surface Plasmon Resonance Imaging, Analytical and Bioanalytical Chemistry, 393(4), 2009, p. 1157–1163. 
27. M. Piliarik, L. Párová, and J. Homola, High-Throughput SPR Sensor for Food Safety, Biosensors and Bioelectronics, 24 (5), 2009, p. 1399–1404. 
28. H. Vaisocherová, Z. Zhang, W. Yang, Z. Cao, G. Cheng, A. D. Taylor, M. Piliarik, J. Homola, and S. Jiang, Functionalizable Surface Platform with Reduced Nonspecific Protein Adsorption from Full Blood Plasma - Material Selection and Protein Immobilization Optimization, Biosensors and Bioelectronics 24(7), 2009, p. 1924–1930. 
29. H. Vaisocherová, W. Yang, Z. Zhang, Z. Cao, G. Cheng, S. Chen, A. D. Taylor, M. Piliarik, J. Homola, and S. Jiang, Ultra-low Fouling and Functionalizable Surface Chemistry Based on a Zwitterionic Polymer Enabling Sensitive and Specific Protein Detection in Undiluted Blood Plasma, Analytical Chemistry, 80(20), 2008, p. 7894–7901. 
30. J. Ladd, A. D. Taylor, M. Piliarik, J. Homola, and S. Jiang, Hybrid Surface Platform for the Simultaneous Detection of Proteins and DNA Using a Surface Plasmon Resonance (SPR) Imaging Sensor, Analytical Chemistry 80(11), 2008, p. 4231–4236. 
31. M. Piliarik, and J. Homola, Self-Referencing SPR Imaging for Most Demanding High Throughput Screening Applications, Sensors and Actuators B-Chemical 134(2), 2008, p. 353–355. 
32. M. Piliarik, H. Vaisocherová, and J. Homola, Towards Parallelized Surface Plasmon Resonance Sensor Platform for Sensitive Detection of Oligonucleotides, Sensors and Actuators B-Chemical, 121(1), 2007, p. 187-193. 
33. H. Vaisocherová, K. Mrkvová, M. Piliarik, P. Jinoch, M. Šteinbachová, and J. Homola, Surface Plasmon Resonance Biosensor for Direct Detection of Antibody Against Epstein-Barr Virus, Biosensors and Bioelectronics 22(6), 2007, p. 1020-1026. 
34. M. Piliarik, H. Vaisocherová and J. Homola, A New Surface Plasmon Resonance Sensor for High-Throughput Screening Applications, Biosensors and Bioelectronics 20(10), 2005, p. 2104-2110. 
35. J. Homola, H. Vaisocherová, J. Dostálek, M. Piliarik, Multi-Analyte Surface Plasmon Resonance Biosensing, Methods 37(1), 2005, p. 26-36. 
36. M. Piliarik, J. Homola , Z. Maníková, J. Čtyroký, Surface Plasmon Resonance Sensor Based on a Single-Mode Polarization-Maintaining Optical Fiber, Sensors and Actuators B 90(1-3), 2003, p. 236-242. 
37. G. G. Nenninger, M. Piliarik, J. Homola, Data Analysis for Optical Sensors Based on Spectroscopy of Surface Plasmons, Measurement Science and Technology 13(12), 2002, p. 2038-2046. 

Proceeding papers:

1. Robert, H., Piliarik, M., Quantitative phase imaging at the nanoscale using interferometric microscope and thermo-optic effect, OSA Imaging and Applied Optics Congress 2021, DW5C.3
2. Čičala, M., Vala, M., Bujak, L., Piliarik, M. Noise characteristics and localisation precision in ultrafast interferometric scattering (iSCAT) microscopy, Proceedings of SPIE - The International Society for Optical Engineering, 2019, 11028, 110282S
3. Jurdová, D., Holanová, K., Vala, M., Piliarik, M., Interferometric scattering (iSCAT) microscopy with optimized reference wave, Proceedings of SPIE - The International Society for Optical Engineering, 2019, 11028, 110282P
4. Bujak, L., Piliarik, M., Interferometric scattering (iSCAT) microscopy for high fidelity tracking at microseconds timescales, Proceedings of SPIE - The International Society for Optical Engineering, 2018, 10726, 1072615
5. M. Piliarik, K. Hegnerová, M. Vala, K. Chadt, I Tichý, J. Homola: Compact multi-channel high-sensitivity biosensor based on spectroscopy of surface plasmons, Proceedings of SPIE - The International Society for Optical Engineering 02/2009, 809216.
6. M. Piliarik, L. Párová, H. Vaisocherová, J. Homola: Surface plasmon resonance imaging for parallelized detection of protein biomarkers, Proceedings of SPIE - The International Society for Optical Engineering 05/2009, 820882.
7. J. Homola, M. Piliarik, P. Kvasnička: Surface Plasmon Resonance Biosensors, Proc. of SPIE Vol. 6619, 2007, 661909-1
8. M. Piliarik, J. Katainen, J.Homola: Novel polarization control for high-throughput surface plasmon resonance sensors, Proceedings of SPIE - The International Society for Optical Engineering 06/2007, 12.724462
9. J. Homola, M. Piliarik, R. Slavik, J. Čtyroký: Advances in development of miniature fiber optic surface plasmon resonance sensors, Proceedings of SPIE - The International Society for Optical Engineering 05/2001; 4416:82-85

Invited and keynote talks:

1. Piliarik, M., Quantitative phase imaging at the nanoscale using interferometric scattering microscope and thermo-optic effect, SPIE Photonics West, 22 - 27 January 2022, San Francisco, 
2. Piliarik, M. Photothermal spatial light modulation enables observing nanoscopic dynamics in slow motion, Invited Talk - Seminar of MST, Center BIOLAS and SPIE Student Chapter, 10.5.2021, Dresden
3. Piliarik, M., Fluctuating dynamics of single disassembling microtubules, Interferometric Scattering Microscopy Workshop, May 26-28 2020, Erlangen, Germany.
4. Piliarik, M. High-fidelity fast tracking of protein motion, 21st Czech-Polish-Slovak Optical Conference on Wave and Quantum Aspects of Contemporary Optics 3. – 7. September, 2018, Lednice, Czechia.
5. M. Piliarik, Single protein detection and single cell analytics, Max-Planck Society – Croucher foundation Joint Workshop on Molecular Systems and Engineering Sciences, April 5 -7, 2016, Hong Kong, China.
6. M. Piliarik, V. Sandoghdar, Label-free single-protein optical biosensing, BIOSENSORS 2012 – 22nd World Congress on Biosensors May 15-18, 2012, Cancun, Mexico.
7. M. Piliarik, The future of label-free optical biosensing: from complex matrices to single protein sensitivity, International workshop of Cancer Diagnosis: Parallel Sensing of Prostate Cancer Biomarkers, January 23, 2014, Bratislava.
8. M. Piliarik, Surface plasmon resonance biosensors for multianalyte detection, 2nd Photonics Global conference, Singapore, 14 – 16 Dec 2010, Book of Abstracts p. 98.

Patents:

1. H. Robert, M. Piliarik: "Thermo-optical spatial light modulator". Czech Patent #308572, 2020.
2. V. Sandoghdar, M. Piliarik, K. König, Method and apparatus for detecting particles, like biological macromolecules or nanoparticles, Japanese patent JP6895951B2
3. J. Homola, M. Piliarik, I. Tichý, M. Vala, P. Adam, J. Hepnar, K. Chadt: Surface Plasmon Resonance Coupler and Disperser Sensor, United States of America Patent # 8,094,316, 2012.
4. M. Piliarik, H. Robert, Thermo-optical spatial light modulator, Pending patent PCT/CZ2020/050072
5. V. Sandoghdar, M. Piliarik, K. König, Method and apparatus for detecting particles, like biological macromolecules or nanoparticles, Pending patent, PCT/EP2015/001804.