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Ducha? M, ?iler M, J\'e1kl P, Brzobohat\'fd O, Rakhubovsky A, Filip R, Zem\'e1nek P. Nanomechanical state amplifier based on optical inverted pendulum. Communications Physics, 8, 276 (2025).\par \par Ghazalova M, Modlitbova P, Samek O, Rebro?ov\'e1 K, ?iler M, Je?ek J, Pil\'e1t Z. Surface-Enhanced Raman Spectroscopy for Adenine Detection in Five Selected Bacterial Strains Under Stress Conditions. SENSORS, 25, 4629 (2025).\par \par Li?ka V, Zem\'e1nkov\'e1 T, J\'e1kl P, ?iler M, Simpson SH, Zem\'e1nek P, Brzobohat\'fd O. PT-like phase transition and limit cycle oscillations in non-reciprocally coupled optomechanical oscillators levitated in vacuum. Nat. Phys., 1?7 (2024).\par \par Stib?rek M, Ondr\'e1?kov\'e1 P, Tuckova T, Turtaev S, ?iler M, Pik\'e1lek T, J\'e1kl P, Gomes A, Krejci J, Kolbabkova P, Uhlirova H, Cizmar T. 110 mu m thin endo-microscope for deep-brain in vivo observations of neuronal connectivity, activity and blood flow dynamics. NATURE COMMUNICATIONS, 14, 1897 (2023).\par \par Koch SMarie, Freidank-Pohl C, Siontas O, Cortesao M, Mota A, Runzheimer K, Jung S, Rebro?ov\'e1 K, ?iler M, Moeller R, Meyer V. Aspergillus niger as a cell factory for the production of pyomelanin, a molecule with UV-C radiation shielding activity. Frontiers in Microbiology, 14, (2023).\par \par Siems K, Runzheimer K, Rebro?ov\'e1 K, Etzbach L, Auerhammer A, Rehm A, Schwengers O, ?iler M, Samek O, R??i?ka F, Moeller R. Identification of staphyloxanthin and derivates in yellow-pigmented Staphylococcus capitis subsp. capitis. Frontiers in Microbiology, 14, (2023).\par \par Bene?ov\'e1 M, Bernatov\'e1 S, Mika F, Pokorn\'e1 Z, Je?ek J, ?iler M, Samek O, R??i?ka F, Rebro?ov\'e1 K, Zem\'e1nek P, Pil\'e1t Z. SERS-Tags: Selective Immobilization and Detection of Bacteria by Strain-Specific Antibodies and Surface-Enhanced Raman Scattering. Biosensors, 13, 182 (2023).\par \par Brzobohat\'fd O, Ducha? M, J\'e1kl P, Je?ek J, ?iler M, Zem\'e1nek P, Simpson SH. Synchronization of spin-driven limit cycle oscillators optically levitated in vacuum. Nature Communications, 14, 5441 (2023).\par \par J\'e1kl P, ?iler M, Je?ek J, Cifuentes A, Tr\'e4g\'e5rdh J, Zem\'e1nek P, Cizmar T. Endoscopic Imaging Using a Multimode Optical Fibre Calibrated with Multiple Internal References. Photonics, 9, 37 (2022).\par \par Kizovsk\'fd M, Pil\'e1t Z, Mylenko M, Hrouzek P, Kuta J, Skoup\'fd R, Krzy?\'e1nek V, Hrubanov\'e1 K, Adamczyk O, Je?ek J, Bernatov\'e1 S, Klementov\'e1 T, Gjevik A, ?iler M, Samek O, Zem\'e1nek P. Raman Microspectroscopic Analysis of Selenium Bioaccumulation by Green Alga Chlorella vulgaris. Biosensors, 11, 115 (2021).\par \par Flaj?manov\'e1 J, ?iler M, Jedli?ka P, Hrub\'fd F, Brzobohat\'fd O, Filip R, Zem\'e1nek P. Using the transient trajectories of an optically levitated nanoparticle to characterize a stochastic Duffing oscillator. Scientific Reports, 10, 14436 (2020).\par \par Rebro?ov\'e1 K, ?iler M, Samek O, R??i?ka F, Bernatov\'e1 S, Je?ek J, Zem\'e1nek P, Hol\'e1 V. Identification of ability to form biofilm in Candida parapsilosis and Staphylococcus epidermidis by Raman spectroscopy. Future Microbiology, 14, 509-517 (2019).\par \par Brzobohat\'fd O, Chv\'e1tal L, Jon\'e1? A, ?iler M, Ka?ka J, Je?ek J, Zem\'e1nek P. Tunable Soft-Matter Optofluidic Waveguides Assembled by Light. ACS Phot., 6, 403-410 (2019).\par \par Pil\'e1t Z, Kizovsk\'fd M, Je?ek J, Kr\'e1tk\'fd S, Sobota J, ?iler M, Samek O, Bury?ka T, Va?\'e1?ek P, Damborsk\'fd J, Prokop Z, Zem\'e1nek P. Detection of chloroalkanes by surface-enhanced raman spectroscopy in microfluidic chips. Sensors, 18, 3212 (2018).\par \par ?iler M, Ornigotti L, Brzobohat\'fd O, J\'e1kl P, Ryabov A, Holubec V, Zem\'e1nek P, Filip R. Diffusing up the Hill: Dynamics and Equipartition in Highly Unstable Systems. Phys. Rev. Lett., 121, 23601 (2018).\par \par Leite IT, Turtaev S, Jiang X, ?iler M, Cuschieri A, Russell PSt. J, ?i?m\'e1r T. Three-dimensional holographic optical manipulation through a high-numerical-aperture soft-glass multimode fibre. Nature Photon., 12, 33?39 (2018).\par \par Svak V, Brzobohat\'fd O, ?iler M, J\'e1kl P, Ka?ka J, Zem\'e1nek P, Simpson SH. Transverse spin forces and non-equilibrium particle dynamics in a circularly polarized vacuum optical trap. Nature Commun., 9, 5453 (2018).\par \par Rebro?ov\'e1 K, ?iler M, Samek O, R??i?ka F, Bernatov\'e1 S, Je?ek J, Zem\'e1nek P, Hol\'e1 V. Differentiation between Staphylococcus aureus and Staphylococcus epidermidis strains using Raman spectroscopy. Future Microbiology, 12, 10 (2017).\par \par Kar\'e1sek V, ?iler M, Brzobohat\'fd O, Zem\'e1nek P. Dynamics of an optically bound structure made of particles of unequal sizes. Opt. Lett., 42, 1436-1439 (2017).\par \par Hrubanov\'e1 K, Krzy?\'e1nek V, Samek O, Skoup\'fd R, ?iler M, Je?ek J, Obru?a S, Zem\'e1nek P. Morphological and Production Changes in Planktonic and Biofilm Cells Monitored Using SEM and Raman Spectroscopy. Microscopy and Microanalysis, 23, S1 (2017).\par \par Rebro?ov\'e1 K, ?iler M, Samek O, R??i?ka F, Bernatov\'e1 S, Hol\'e1 V, Je?ek J, Zem\'e1nek P, Sokolov\'e1 J, Petr\'e1? P. Rapid identification of staphylococci by Raman spectroscopy. Sci. Rep., 7, 14846 (2017).\par \par ?iler M, J\'e1kl P, Brzobohat\'fd O, Ryabov A, Filip R, Zem\'e1nek P. Thermally induced micro-motion by inflection in optical potential. Sci. Rep., 7, 1697 (2017).\par \par ?iler M, Je?ek J, J\'e1kl P, Pil\'e1t Z, Zem\'e1nek P. Direct measurement of the temperature profile close to an optically trapped absorbing particle. Opt. Lett., 41, 870-873 (2016).\par \par Zem\'e1nek P, ?iler M, Brzobohat\'fd O, J\'e1kl P, Filip R. Noise-to-signal transition of a Brownian particle in the cubic potential: II. optical trapping geometry. Journal of Optics, 18, 065402 (2016).\par \par Samek O, Obru?a S, ?iler M, Sedl\'e1?ek P, Bene?ov\'e1 P, Ku?era D, M\'e1rov\'e1 I, Je?ek J, Bernatov\'e1 S, Zem\'e1nek P. Quantitative Raman Spectroscopy Analysis of Polyhydroxyalkanoates Produced by Cupriavidus necator H16. Sensors, 16, 1808 (2016).\par \par Bar\'e1nek M, Bouchal P, ?iler M, Bouchal Z. Aberration resistant axial localization using a self-imaging of vortices. Opt. Express, 23, 15316?15331 (2015).\par \par Brzobohat\'fd O, Arzola AV, ?iler M, Chv\'e1tal L, J\'e1kl P, Simpson SH, Zem\'e1nek P. Complex rotational dynamics of multiple spheroidalparticles in a circularly polarized, dual beam trap. Opt. Express, 23, 7273-7287 (2015).\par \par Krzy?\'e1nek V, Hrubanov\'e1 K, Samek O, Obru?a S, M\'e1rov\'e1 I, Bernatov\'e1 S, ?iler M, Zem\'e1nek P. Cryo-SEM and Raman Spectroscopy Study of the Involvement of Polyhydroxyalkanoates in Stress Response of Bacteria. Microscopy and Microanalysis, 21, 183-184 (2015).\par \par Samek O, Bernatov\'e1 S, Je?ek J, ?iler M, ?er\'fd M, Krzy?\'e1nek V, Hrubanov\'e1 K, Zem\'e1nek P, Hol\'e1 V, R??i?ka F. Identification of individual biofilm-forming bacterial cells using Raman tweezers. J. Biomed. Opt., 20, (2015).\par \par Mlynarikov\'e1 K, Samek O, Bernatov\'e1 S, R??i?ka F, Je?ek J, Haronikov\'e1 A, ?iler M, Zem\'e1nek P, Hol\'e1 V. Influence of Culture Media on Microbial Fingerprints Using Raman Spectroscopy. Sensors, 15, 29635-29647 (2015).\par \par Brzobohat\'fd O, ?iler M, Trojek J, Chv\'e1tal L, Kar\'e1sek V, Zem\'e1nek P. Non-spherical gold nanoparticles trapped in optical tweezers: shape matters. Opt. Express, 23, 8179-8189 (2015).\par \par ?iler M, Zem\'e1nek P. Optical trapping in secondary maxima of focused laser beam. J. Quant. Spectrosc. Radiat. Transf., 162, 114 - 121 (2015).\par \par Brzobohat\'fd O, ?iler M, Trojek J, Chv\'e1tal L, Kar\'e1sek V, Pat\'e1k A, Pokorn\'e1 Z, Mika F, Zem\'e1nek P. Three-Dimensional Optical Trapping of a Plasmonic Nanoparticle using Low Numerical Aperture Optical Tweezers. Sci. Rep., 5, 8106 (2015).\par \par Samek O, Mlynarikov\'e1 K, Bernatov\'e1 S, Je?ek J, Krzy?\'e1nek V, ?iler M, Zem\'e1nek P, R??i?ka F, Hol\'e1 V, Mahelov\'e1 M. Candida parapsilosis Biofilm Identification by RamanSpectroscopy. Int. J. Mol. Sci., 15, 23924-23935 (2014).\par \par J\'e1kl P, Arzola AV, ?iler M, Chv\'e1tal L, Volke-Sep\'falveda K, Zem\'e1nek P. Optical sorting of nonspherical and living microobjects in moving interference structures. Opt. Express, 22, 29746-29760 (2014).\par \par Brzobohat\'fd O, Kar\'e1sek V, ?iler M, Chv\'e1tal L, ?i?m\'e1r T, Zem\'e1nek P. Experimental demonstration of optical transport, sorting and self-arrangement using a `tractor beam'. Nature Photon., 7, 123-127 (2013).\par \par Bernatov\'e1 S, Samek O, Pil\'e1t Z, ?er\'fd M, Je?ek J, J\'e1kl P, ?iler M, Krzy?\'e1nek V, Zem\'e1nek P, Hol\'e1 V, Dvo?\'e1?kov\'e1 M, R??i?ka F. Following the mechanisms of bacteriostatic versus bacericidal action using Raman spectroscopy. Molecules, 18, 13188-13199 (2013).\par \par ?iler M, Chv\'e1tal L, Zem\'e1nek P. Metallic nanoparticles in a standing wave: optical forceand heating. J. Quant. Spectrosc. Radiat. Transf., 126, 84-90 (2013).\par \par ?iler M, Zem\'e1nek P. Optical forces in a non-diffracting vortex beam. J. Quant. Spectrosc. Radiat. Transf., 126, 78-83 (2013).\par \par Brzobohat\'fd O, ?iler M, Je?ek J, J\'e1kl P, Zem\'e1nek P. Optical manipulation of aerosol droplets using aholographic dual and single beam trap. Opt. Lett., 38, 4601-4604 (2013).\par \par ?iler M, J\'e1kl P, Brzobohat\'fd O, Zem\'e1nek P. Optical forces induced behavior of a particle in a non-diffracting vortex beam. Opt. Express, 20, 24304-24319 (2012).\par \par ?iler M, ?i?m\'e1r T, Zem\'e1nek P. Speed enhancement of multi-particle chain in a travelingstanding wave. Appl. Phys. Lett., 100, 051103 (2012).\par \par ?iler M, Zem\'e1nek P. Parametric study of optical forces acting upon nanoparticles in a single, or a standing, evanescentwave. J. Opt., 13, 044016:1?9 (2011).\par \par Brzobohat\'fd O, Kar\'e1sek V, ?iler M, Trojek J, Zem\'e1nek P. Static and dynamic behavior of two optically boundmicroparticles in a standing wave. Opt. Express, 19, 19613?19626 (2011).\par \par Brzobohat\'fd O, ?i?m\'e1r T, Kar\'e1sek V, ?iler M, Dholakia K, Zem\'e1nek P. Experimental and theoretical determination of opticalbinding forces. Opt. Express, 18, 25389?25402 (2010).\par \par ?iler M, Zem\'e1nek P. Particle jumps between optical traps in a one-dimensionaloptical lattice. New. J. Phys., 12, 083001:1?20 (2010).\par \par ?iler M, ?i?m\'e1r T, Jon\'e1? A, Zem\'e1nek P. Surface delivery of a single nanoparticle under movingevanescent standing-wave illumination. New. J. Phys., 10, 113010 (2008).\par \par ?iler M, Zem\'e1nek P. Optical forces acting on a nanoparticle placed into an interference evanescent field. Opt. Commun., 275, 409?420 (2007).\par \par ?iler M, ?i?m\'e1r T, ?er\'fd M, Zem\'e1nek P. Optical forces generated by evanescent standing waves and their usage for sub-micron particle delivery. Appl. Phys. B, 84, 157?165 (2006).\par \par ?i?m\'e1r T, ?iler M, Zem\'e1nek P. An optical nanotrap array movable over a milimetre range. Appl. Phys. B, 84, 197?203 (2006).\par \par ?i?m\'e1r T, ?iler M, ?er\'fd M, Zem\'e1nek P, Garc\'e9s-Ch\'e1vez V, Dholakia K. Optical sorting and detection of sub-micron objects in a motional standing wave. Phys. Rev. B, 74, 035105:1-6 (2006).\par \par }