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2025
Laznicka T, Kizovský M, Hrubanová K, Ježek J, Mrazova K, Obruča S, Samek O, Krzyžánek V. Assembly for semi-correlation analysis of samples using cryogenic scanning electron microscopy and cryogenic Raman micro-spectroscopy. MEASUREMENT SCIENCE AND TECHNOLOGY, 36, 055903 (2025).
Pořízka P, Holub D, Kizovský M, Samek O, Kaiser J, Kalčíková G. Chapter 26 - Hyphenated Raman and laser spectroscopy for the characterization of microplastics in tissues. Applied Raman Spectroscopy. (Singh VKumared.), Elsevier, s.441-451 (2025).
Silhan L, Arregi JAnder, Plichta T, Vaculik O, Novotny J, Šerý M. Compact vacuum setup for laser induced plasma etching with optical emission spectrum monitoring. Journal of Vacuum Science & Technology B, 43, 034202 (2025).
Brzobohatý O, Chvátal L, Jonáš A, Zemánek P. Dynamic formation of arrays of interacting optical spatial solitons under light-sheet illumination. Optics Letters, 50, 4318–4321 (2025).
Richterová V, Gjevik A, Vaculik O, Vejrosta J, Pekař M. Impact of Collagen on the Rheological and Transport Properties of Agarose Hydrogels. Gels, 11, 396 (2025).
Duchaň M, Šiler M, Jákl P, Brzobohatý O, Rakhubovsky A, Filip R, Zemánek P. Nanomechanical state amplifier based on optical inverted pendulum. Communications Physics, 8, 276 (2025).
Vejrosta J, Cabalová S, Plichta T, Šerý M, Maňka T, Samek O, Zemánek P. Preparation and pilot experiments on microfluidic chip with surface acoustic waves, 23rd Slovak-Czech-Polish Optical Conference on Wave and Quantum Aspects of Contemporary Optics, (Pudiš D, Jandura D, Lettrichová Ied.), 2025, International Society for Optics and Photonics.
Heinke R, Šilhan L, Ehrhardt M, Lorenz P, Zajadacz J, Bauer J, Arnold T, Šerý M, Zimmer K. Stability of masking materials for pattern transfer of lithographic masks into fused silica by atmospheric pressure plasma jet etching. Micro and Nano Engineering, 28, 100309 (2025).
Ghazalova M, Modlitbova P, Samek O, Rebrošová K, Šiler M, Ježek J, Pilát Z. Surface-Enhanced Raman Spectroscopy for Adenine Detection in Five Selected Bacterial Strains Under Stress Conditions. SENSORS, 25, 4629 (2025).
2024
Jones P, Bernatová S, Kotsifaki DG. Biomedical Optics Express Feature Issue Introduction: Optical Manipulation and Its Applications (OMA) 2023. BIOMEDICAL OPTICS EXPRESS, 15, 1192-1194 (2024).
Silhan L, Novotny J, Plichta T, Ježek J, Vaculik O, Šerý M. Design of Setup for Laser Induced Plasma Etching, 2024 37th International Vacuum Nanoelectronics Conference (IVNC), 2024.
Uhlirova H, Cizmar T, Pakan JMP, Gomes A. Exploiting Complex Media Photonics to Illuminate Brain's Hidden Depth. NEUROPHOTONICS, 11, S11501 (2024).
Plichta T, Čech V. Functional Interlayers Developed to Control Interfacial Adhesion in Polymer Composites Reinforced with Glass and Basalt Fibers. Progress in Adhesion and Adhesives. Vol. 8. (Mittal KLed.) Kap. 3, Wiley, s.119–188 (2024).
Michálková I, Colombel S, Gomes AD, Cizmar T. Generating Airy beams through multimode fibres. Optics Express, 32, 6838–6847 (2024).
Lee KSoo, Landry Z, Athar A, Alcolombri U, Ayutthaya PPramoj Na, Berry D, de Bettignies P, Cheng J-X, Csucs G, Cui L, Deckert V, Dieing T, Dionne J, Doskocil O, D'Souza G, Garcia-Timermans C, Gierlinger N, Goda K, Hatzenpichler R, Henshaw RJ, Huang WE, Iermak I, Ivleva NP, Kneipp J, Kubryk P, Kuesel K, Lee TKwon, Lee SSik, Ma B, Martinez-Perez C, Matousek P, Meckenstock RU, Min W, Mojzes P, Mueller O, Kumar N, Nielsen PHalkjaer, Notingher I, Palatinszky M, Pereira FC, Pezzotti G, Pilát Z, Plesinger F, Popp J, Probst AJ, Riva A, Saleh AAE, Samek O, Sapers HM, Schubert OT, Stubbusch AKM, Tadesse LF, Taylor GT, Wagner M, Wang J, Yin H, Yue Y, Zenobi R, Zini J, Sarkans U, Stocker R. MicrobioRaman: an open-access web repository for microbiological Raman spectroscopy data. NATURE MICROBIOLOGY, 9, (2024).
Khan A, Qadeer A, Wajid A, Ullah Q, Rahman SUr, Ullah K, Safi SZaman, Ticha L, Skalickova S, Chilala P, Bernatová S, Samek O, Horky P. Microplastics in animal nutrition: Occurrence, spread, and hazard in animals. JOURNAL OF AGRICULTURE AND FOOD RESEARCH, 17, 101258 (2024).
Liška V, Zemánková T, Jákl P, Šiler M, Simpson SH, Zemánek P, Brzobohatý O. PT-like phase transition and limit cycle oscillations in non-reciprocally coupled optomechanical oscillators levitated in vacuum. Nat. Phys., 1–7 (2024).
Parobková V, Holub D, Kizovský M, Kalčíková G, Rozman U, Urík M, Novotný K, Samek O, Zikmund T, Pořízka P, Kaiser J. Raman microspectroscopy and laser-induced breakdown spectroscopy for the analysis of polyethylene microplastics in human soft tissues. Heliyon, 10, e37844 (2024).
Maňka T, Šiler M, Liška V, Zemánek P, Šerý M, Brzobohatý O. Simulation of optomechanical interaction of levitated nanoparticle with photonic crystal micro cavity. Opt. Express, 32, 7185–7196 (2024).
Uhlirova H, Stibůrek M, Pikálek T, Gomes A, Turtaev S, Kolbabkova P, Cizmar T. ``There's plenty of room at the bottom'': deep brain imaging with holographic endo-microscopy. NEUROPHOTONICS, 11, (2024).
Naz S, Chatha AManan Must, Khan NAhmed, Ullah Q, Zaman F, Qadeer A, Khan IMuhammad, Danabas D, Kiran A, Skalickova S, Bernatová S, Khan MZahoor, Horky P. Unraveling the ecotoxicological effects of micro and nano-plastics on aquatic organisms and human health. Frontiers in Environmental Science, 12, (2024).
2023
Stibůrek M, Ondráčková P, Tuckova T, Turtaev S, Šiler M, Pikálek T, Jákl 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).
Mouralova K, Benes L, Prokes T, Zahradnicek R, Fries J, Plichta T. Analysis of the machinability of different types of sintered carbides with WEDM in both water and oil baths. The International Journal of Advanced Manufacturing Technology, (2023).
Ozbakir Y, Jonas A, Kiraz A, Erkey C. Application of Aerogels in Optical Devices. Springer Handbook of Aerogels. (Aegerter MA, Leventis N, Koebel M, III SASteinered.), Springer International Publishing, Cham, s.1431–1454 (2023).
Koch SMarie, Freidank-Pohl C, Siontas O, Cortesao M, Mota A, Runzheimer K, Jung S, Rebrošová K, Šiler 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).
Šiler M, Svak V, Jonáš A, Simpson SH, Brzobohatý O, Zemánek P. Bayesian Estimation of Experimental Parameters in Stochastic Inertial Systems: Theory, Simulations, and Experiments with Objects Levitated in Vacuum. Phys. Rev. Appl., 19, 064059 (2023).
Liška V, Zemánková T, Svak V, Jákl P, Ježek J, Bránecký M, Simpson SH, Zemánek P, Brzobohatý O. Cold damping of levitated optically coupled nanoparticles. Optica, 10, 1203–1209 (2023).
Arita Y, Simpson SH, Bruce GD, Wright EM, Zemánek P, Dholakia K. Cooling the optical-spin driven limit cycle oscillations of a levitated gyroscope. Commun. Phys., 6, 238 (2023).
Brodský J, Gablech I, Migliaccio L, Havli'cek M, Donahue MJJ, Glowacki EDD. Downsizing the Channel Length of Vertical Organic Electrochemical Transistors. ACS APPLIED MATERIALS & INTERFACES, 15, 27002-27009 (2023).
Siems K, Runzheimer K, Rebrošová K, Etzbach L, Auerhammer A, Rehm A, Schwengers O, Šiler M, Samek O, Růžička F, Moeller R. Identification of staphyloxanthin and derivates in yellow-pigmented Staphylococcus capitis subsp. capitis. Frontiers in Microbiology, 14, (2023).
Pořízka P, Brunnbauer L, Porkert M, Rozman U, Marolt G, Holub D, Kizovský M, Benešová M, Samek O, Limbeck A, Kaiser J, Kalčíková G. Laser-based techniques: Novel tools for the identification and characterization of aged microplastics with developed biofilm. Chemosphere, 313, 137373 (2023).
Tarbajova V, Kolackova M, Chaloupsky P, Dobesova M, Capal P, Pilat Z, Samek O, Zemánek P, Svec P, Sterbova DSkopalova, Vaculovicova M, Richtera L, Pérez-de-Mora A, Adam V, Huska D. Physiological and transcriptome profiling of Chlorella sorokiniana: A study on azo dye wastewater decolorization. Journal of Hazardous Materials, 460, 132450 (2023).
Rebrošová K, Bernatová S, Šiler M, Mašek J, Samek O, Ježek J, Kizovský M, Holá V, Zemánek P, Růžička F. Rapid Identification of Pathogens Causing Bloodstream Infections by Raman Spectroscopy and Raman Tweezers. Microbiology Spectrum, 11, e00028-23 (2023).
Vaculík O, Bernatová S, Rebrošová K, Samek O, Šilhan L, žička FRů, Šerý M, Šiler M, ek JJež, Zemánek P. Rapid identification of pathogens in blood serum via Raman tweezers in combination with advanced processing methods. Biomed. Opt. Express, 14, 6410–6421 (2023).
Volpe G, Maragò OM, Rubinsztein-Dunlop H, Pesce G, Stilgoe AB, Volpe G, Tkachenko G, Truong VGiang, Chormaic SNic, Kalantarifard F, Elahi P, Käll M, Callegari A, Marqués MI, Neves AAR, Moreira WL, Fontes A, Cesar CL, Saija R, Saidi A, Beck P, Eismann JS, Banzer P, Fernandes TFD, Pedaci F, Bowen WP, Vaippully R, Lokesh M, Roy B, Thalhammer-Thurner G, Ritsch-Marte M, García LPérez, Arzola AV, Castillo IPérez, Argun A, Muenker TM, Vos BE, Betz T, Cristiani I, Minzioni P, Reece PJ, Wang F, McGloin D, Ndukaife JC, Quidant R, Roberts RP, Laplane C, Volz T, Gordon R, Hanstorp D, Marmolejo JTello, Bruce GD, Dholakia K, Li T, Brzobohatý O, Simpson SH, Zemánek P, Ritort F, Roichman Y, Bobkova V, Wittkowski R, Denz C, Kumar GVPavan, Foti A, Donato MGrazia, Gucciardi PG, Gardini L, Bianchi G, Kashchuk AV, Capitanio M, Paterson L, Jones PH, Berg-Sørensen K, Barooji YF, Oddershede LB, Pouladian P, Preece D, Adiels CBeck, De Luca AChiara, Magazzù A, Ciriza DBronte, Iatì MAntonia, Swartzlander GA. Roadmap for optical tweezers. Journal of Physics: Photonics, 5, 022501 (2023).
Benešová M, Bernatová S, Mika F, Pokorná Z, Ježek J, Šiler M, Samek O, Růžička F, Rebrošová K, Zemánek P, Pilát Z. SERS-Tags: Selective Immobilization and Detection of Bacteria by Strain-Specific Antibodies and Surface-Enhanced Raman Scattering. Biosensors, 13, 182 (2023).
Plichta T, Sulc V, Ohlidal M, Cech V. Stable a-CSi:H films with a wide range of modulus of elasticity and low internal stress. Surface and Coatings Technology, 459, 129147 (2023).
Brzobohatý O, Duchaň M, Jákl P, Ježek J, Šiler M, Zemánek P, Simpson SH. Synchronization of spin-driven limit cycle oscillators optically levitated in vacuum. Nature Communications, 14, 5441 (2023).
2022
Hrabina J, Hosek M, Rerucha S, Cizek M, Pilat Z, Zucco M, Lazar J, Cip O. Absolute frequencies of H13C14N hydrogen cyanide transitions in the 1.5-µm region with the saturated spectroscopy and a sub-kHz scanning laser. Opt. Lett., 47, 5704–5707 (2022).
Arita Y, Bruce GD, Wright EM, Simpson SH, Zemánek P, Dholakia K. All-optical sub-Kelvin sympathetic cooling of a levitated microsphere in vacuum. Optica, 9, 1000–1002 (2022).
Violi IL, Martinez LP, Barella M, Zaza C, Chvátal L, Zemánek P, Gutierrez MV, Paredes MY, Scarpettini AF, Olmos-Trigo J, Pais VR, Noblega IDiaz, Cortès E, Saenz JJose, Bragas AV, Gargiulo J, Stefani FD. Challenges on optical printing of colloidal nanoparticles. J. Chem. Phys., 156, 034201 (2022).
Endoscopic Imaging Using a Multimode Optical Fibre Calibrated with Multiple Internal References. Photonics, 9, 37 (2022).
Mouralova K, Michna S, Zahradnicek R, Bednar J, Plichta T, Fries J. Experimental analysis of microhardness changes of subsurface areas affected by WEDM. Proceedings of the Institution of Mechanical Engineers, Part E: Journal of Process Mechanical Engineering, 236, 1979-1991 (2022).
Meixner K, Daffert C, Dalnodar D, Mrazova K, Hrubanová K, Krzyzanek V, Nebesářová J, Samek O, Sedrlova Z, Slaninová E, Sedláček P, Obruča S, Fritz I. Glycogen, poly(3-hydroxybutyrate) and pigment accumulation in three Synechocystis strains when exposed to a stepwise increasing salt stress. JOURNAL OF APPLIED PHYCOLOGY, 34, 1227-1241 (2022).
Būtaitė UG, Kupianskyi H, Cizmar T, Phillips DB. How to Build the ``Optical Inverse'' of a Multimode Fibre. Intelligent Computing, 2022, 9816026 (2022).
Du Y, Turtaev S, Leite IT, Lorenz A, Kobelke J, Wondraczek K, Čižmár T. Hybrid multimode - multicore fibre based holographic endoscope for deep-tissue neurophotonics. Light: Advanced Manufacturing, 3, 1 (2022).
Karalko A, Kesa P, Jelinek F, Sefc L, Ježek J, Zemánek P, Grus T. In Vivo Contrast Imaging of Rat Heart with Carbon Dioxide Foam. SENSORS, 22, 5124 (2022).
Cifuentes A, Trägårdh J. A method for single particle tracking through a multimode fiber. Opt. Express, 30, 36055–36064 (2022).
Gomes AD, Turtaev S, Du Y, Čižmár T. Near perfect focusing through multimode fibres. Opt. Express, 30, 10645–10663 (2022).
Abdelfattah A, Ahuja S, Akkin T, Allu SRao, Boas DA, Brake J, Buckley EM, Campbell RE, Chen AI, Cheng X, Čižmár T, Costantini I, De Vittorio M, Devor A, Doran PR, Khatib MEl, Emiliani V, Fomin-Thunemann N, Fainman Y, Alfonso TFernández, Ferri CGL, Gilad A, Han X, Harris A, Hillman EMC, Hochgeschwender U, Holt MG, Ji N, Kiliç K, Lake EMR, Li L, Li T, Mächler P, Mesquita RC, Miller EW, Nadella KMNaga Srini, U. Nägerl V, Nasu Y, Nimmerjahn A, Ondráčková P, Pavone FS, Campos CPerez, Peterka DS, Pisano F, Pisanello F, Puppo F, Sabatini BL, Sadegh S, Sakadžic S, Shoham S, Shroff SN, R. Silver A, Sims RR, Smith SL, Srinivasan VJ, Thunemann M, Tian L, Tian L, Troxler T, Valera A, Vaziri A, Vinogradov SA, Vitale F, Wang LV, Uhlířová H, Xu C, Yang C, Yang M-H, Yellen G, Yizhar O, Zhao Y. Neurophotonic tools for microscopic measurements and manipulation: status report. Neurophotonics, 9, (2022).

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