%0 Journal Article %J Opt. Express %D 2024 %T Simulation of optomechanical interaction of levitated nanoparticle with photonic crystal micro cavity %A Tadeáš Maňka %A Martin Šiler %A Vojtěch Liška %A Pavel Zemánek %A Mojmír Šerý %A Oto Brzobohatý %K LF %K MF %X

We propose and analyze theoretically a promising design of an optical trap for vacuum levitation of nanoparticles based on a one-dimensional (1D) silicon photonic crystal cavity (PhC). The considered cavity has a quadratically modulated width of the silicon wave guiding structure, leading to a calculated cavity quality factor of 8 × 105. An effective mode volume of approximately 0.16 μm3 having the optical field strongly confined outside the silicon structure enables optical confinement on nanoparticle in all three dimensions. The optical forces and particle-cavity optomechanical coupling are comprehensively analyzed for two sizes of silica nanoparticles (100 nm and 150 nm in diameter) and various mode detunings. The value of trapping stiffnesses in the microcavity is predicted to be 5 order of magnitudes higher than that reached for optimized optical tweezers, moreover the linear single photon coupling rate can reach MHz level which is 6 order magnitude larger than previously reported values for common bulk cavities. The theoretical results support optimistic prospects towards a compact chip for optical levitation in vacuum and cooling of translational mechanical degrees of motion for the silica nanoparticle of a diameter of 100 nm.

%B Opt. Express %V 32 %P 7185–7196 %8 Feb %G eng %U https://opg.optica.org/oe/abstract.cfm?URI=oe-32-5-7185 %R 10.1364/OE.515202 %0 Journal Article %J NATURE COMMUNICATIONS %D 2023 %T 110 mu m thin endo-microscope for deep-brain in vivo observations of neuronal connectivity, activity and blood flow dynamics %A Stibůrek, Miroslav %A Ondráčková, Petra %A Tuckova, Tereza %A Turtaev, Sergey %A Šiler, Martin %A Pikálek, Tomáš %A Jákl, Petr %A Gomes, Andre %A Krejci, Jana %A Kolbabkova, Petra %A Uhlirova, Hana %A Cizmar, Tomas %K KF %K MF %B NATURE COMMUNICATIONS %V 14 %P 1897 %8 APR 5 %G eng %R 10.1038/s41467-023-36889-z %0 Journal Article %J The International Journal of Advanced Manufacturing Technology %D 2023 %T Analysis of the machinability of different types of sintered carbides with WEDM in both water and oil baths %A Mouralova, Katerina %A Benes, Libor %A Prokes, Tomas %A Zahradnicek, Radim %A Fries, Jiri %A Plichta, Tomáš %K AIF %K MF %X

The unconventional wire electric discharge machining (WEDM) technology represents a vital manufacturing technology in different industrial branches. This technology is essential because of the possibility to machine difficult-to-machine materials such as sintered carbides. For this reason, this study analyses the machinability of sintered carbides WKP23S, WSM33S and WK1 with WEDM in both water and oil baths. We investigated the influence of the machining parameters, namely, pulse off time, gap voltage, discharge current, pulse on time and wire feed, on the cutting speed, surface roughness and defect occurrence. We investigated 9 different roughness parameters, analysed surface morphology with an electron microscope and also analysed cross-sectioned samples. We found out that machining sintered carbides in oil bath yields better results than machining in deionized water. The oil tank prevents the removal of the cobalt binder, but it does not reduce fissure occurrence in any significant way. The lowest Ra value, that is 0.7 µm, was recorded for the WKP23S sample when machined in oil and Ra 0.9 µm when the same material was machined in water.

%B The International Journal of Advanced Manufacturing Technology %G eng %U https://doi.org/10.1007/s00170-023-10913-4 %R 10.1007/s00170-023-10913-4 %0 Book Section %B Springer Handbook of Aerogels %D 2023 %T Application of Aerogels in Optical Devices %A Ozbakir, Yaprak %A Jonas, Alexandr %A Kiraz, Alper %A Erkey, Can %E Aegerter, Michel A. %E Leventis, Nicholas %E Koebel, Matthias %E Steiner III, Stephen A. %K LF %K MF %B Springer Handbook of Aerogels %I Springer International Publishing %C Cham %P 1431–1454 %@ 978-3-030-27322-4 %G eng %U https://doi.org/10.1007/978-3-030-27322-4_56 %R 10.1007/978-3-030-27322-4_56 %0 Journal Article %J Frontiers in Microbiology %D 2023 %T Aspergillus niger as a cell factory for the production of pyomelanin, a molecule with UV-C radiation shielding activity %A Koch, Stella Marie %A Freidank-Pohl, Carsten %A Siontas, Oliver %A Cortesao, Marta %A Mota, Afonso %A Runzheimer, Katharina %A Jung, Sascha %A Rebrošová, Katarína %A Šiler, Martin %A Moeller, Ralf %A Meyer, Vera %K BF %K MF %B Frontiers in Microbiology %V 14 %G eng %U https://www.frontiersin.org/articles/10.3389/fmicb.2023.1233740 %R 10.3389/fmicb.2023.1233740 %0 Journal Article %J Phys. Rev. Appl. %D 2023 %T Bayesian Estimation of Experimental Parameters in Stochastic Inertial Systems: Theory, Simulations, and Experiments with Objects Levitated in Vacuum %A Šiler, M. %A Svak, V. %A Jonáš, A. %A Simpson, S.H. %A Brzobohatý, O. %A Zemánek, P. %K LF %K MF %B Phys. Rev. Appl. %V 19 %P 064059 %8 Jun %G eng %U https://link.aps.org/doi/10.1103/PhysRevApplied.19.064059 %R 10.1103/PhysRevApplied.19.064059 %0 Journal Article %J Optica %D 2023 %T Cold damping of levitated optically coupled nanoparticles %A Vojtěch Liška %A Tereza Zemánková %A Vojtech Svak %A Petr Jákl %A Jan Ježek %A Martin Bránecký %A Stephen H. Simpson %A Pavel Zemánek %A Oto Brzobohatý %K LF %K MF %B Optica %V 10 %P 1203–1209 %G eng %U https://opg.optica.org/optica/abstract.cfm?URI=optica-10-9-1203 %R 10.1364/OPTICA.496072 %0 Journal Article %J Commun. Phys. %D 2023 %T Cooling the optical-spin driven limit cycle oscillations of a levitated gyroscope %A Yoshihiko Arita %A Stephen H. Simpson %A Graham D. Bruce %A Ewan M. Wright %A Pavel Zemánek %A Kishan Dholakia %K LF %K MF %B Commun. Phys. %V 6 %P 238 %8 Nov %G eng %0 Journal Article %J ACS APPLIED MATERIALS & INTERFACES %D 2023 %T Downsizing the Channel Length of Vertical Organic Electrochemical Transistors %A Brodský, Jan %A Gablech, Imrich %A Migliaccio, Ludovico %A Havli'cek, Marek %A Donahue, Mary J. J. %A Glowacki, Eric D. D. %K KF %K MF %X

Organic electrochemical transistors (OECTs) are promisingbuildingblocks for bioelectronic devices such as sensors and neural interfaces.While the majority of OECTs use simple planar geometry, there is interestin exploring how these devices operate with much shorter channelson the submicron scale. Here, we show a practical route toward theminimization of the channel length of the transistor using traditionalphotolithography, enabling large-scale utilization. We describe thefabrication of such transistors using two types of conducting polymers.First, commercial solution-processed poly-(dioxyethylenethiophene):poly-(styrenesulfonate), PEDOT:PSS. Next, we also exploit the short channel lengthto support easy in situ electropolymerization of poly-(dioxyethylenethiophene):tetrabutylammonium hexafluorophosphate, PEDOT:PF6. Both variantsshow different promising features, leading the way in terms of transconductance(g (m)), with the measured peak g (m) up to 68 mS for relatively thin (280 nm) channel layerson devices with the channel length of 350 nm and with widths of 50,100, and 200 mu m. This result suggests that the use of electropolymerizedsemiconductors, which can be easily customized, is viable with verticalgeometry, as uniform and thin layers can be created. Spin-coated PEDOT:PSSlags behind with the lower values of g (m); however, it excels in terms of the speed of the device and alsohas a comparably lower off current (300 nA), leading to unusuallyhigh on/off ratio, with values up to 8.6 x 10(4). Ourapproach to vertical gap devices is simple, scalable, and can be extendedto other applications where small electrochemical channels are desired.

%B ACS APPLIED MATERIALS & INTERFACES %V 15 %P 27002-27009 %8 MAY 22 %G eng %9 Article %R 10.1021/acsami.3c02049 %0 Journal Article %J Frontiers in Microbiology %D 2023 %T Identification of staphyloxanthin and derivates in yellow-pigmented Staphylococcus capitis subsp. capitis %A Siems, Katharina %A Runzheimer, Katharina %A Rebrošová, Katarína %A Etzbach, Lara %A Auerhammer, Alina %A Rehm, Anna %A Schwengers, Oliver %A Šiler, Martin %A Samek, Ota %A Růžička, Filip %A Moeller, Ralf %K BF %K MF %B Frontiers in Microbiology %V 14 %G eng %U https://www.frontiersin.org/articles/10.3389/fmicb.2023.1272734 %R 10.3389/fmicb.2023.1272734 %0 Journal Article %J Chemosphere %D 2023 %T Laser-based techniques: Novel tools for the identification and characterization of aged microplastics with developed biofilm %A Pavel Pořízka %A Lukas Brunnbauer %A Michaela Porkert %A Ula Rozman %A Gregor Marolt %A Daniel Holub %A Martin Kizovský %A Markéta Benešová %A Ota Samek %A Andreas Limbeck %A Jozef Kaiser %A Gabriela Kalčíková %K BF %K MF %X

Microplastics found in the environment are often covered with a biofilm, which makes their analysis difficult. Therefore, the biofilm is usually removed before analysis, which may affect the microplastic particles or lead to their loss during the procedure. In this work, we used laser-based analytical techniques and evaluated their performance in detecting, characterizing, and classifying pristine and aged microplastics with a developed biofilm. Five types of microplastics from different polymers were selected (polyamide, polyethylene, polyethylene terephthalate, polypropylene, and polyvinyl chloride) and aged under controlled conditions in freshwater and wastewater. The development of biofilm and the changes in the properties of the microplastic were evaluated. The pristine and aged microplastics were characterized by standard methods (e.g., optical and scanning electron microscopy, and Raman spectroscopy), and then laser-induced breakdown spectroscopy (LIBS) and laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) were used. The results show that LIBS could identify different types of plastics regardless of the ageing and major biotic elements of the biofilm layer. LA-ICP-MS showed a high sensitivity to metals, which can be used as markers for various plastics. In addition, LA-ICP-MS can be employed in studies to monitor the adsorption and desorption (leaching) of metals during the ageing of microplastics. The use of these laser-based analytical techniques was found to be beneficial in the study of environmentally relevant microplastics.

%B Chemosphere %V 313 %P 137373 %G eng %U https://www.sciencedirect.com/science/article/pii/S0045653522038668 %R https://doi.org/10.1016/j.chemosphere.2022.137373 %0 Journal Article %J Journal of Hazardous Materials %D 2023 %T Physiological and transcriptome profiling of Chlorella sorokiniana: A study on azo dye wastewater decolorization %A Vladimira Tarbajova %A Martina Kolackova %A Pavel Chaloupsky %A Marketa Dobesova %A Petr Capal %A Zdenek Pilat %A Ota Samek %A Pavel Zemánek %A Pavel Svec %A Dagmar Skopalova Sterbova %A Marketa Vaculovicova %A Lukas Richtera %A Alfredo Pérez-de-Mora %A Vojtech Adam %A Dalibor Huska %K BF %K MF %X

Over decades, synthetic dyes have become increasingly dominated by azo dyes posing a significant environmental risk due to their toxicity. Microalgae-based systems may offer an alternative for treatment of azo dye effluents to conventional physical-chemical methods. Here, microalgae were tested to decolorize industrial azo dye wastewater (ADW). Chlorella sorokiniana showed the highest decolorization efficiency in a preliminary screening test. Subsequently, the optimization of the experimental design resulted in 70% decolorization in a photobioreactor. Tolerance of this strain was evidenced using multiple approaches (growth and chlorophyll content assays, scanning electron microscopy (SEM), and antioxidant level measurements). Raman microspectroscopy was employed for the quantification of ADW-specific compounds accumulated by the microalgal biomass. Finally, RNA-seq revealed the transcriptome profile of C. sorokiniana exposed to ADW for 72 h. Activated DNA repair and primary metabolism provided sufficient energy for microalgal growth to overcome the adverse toxic conditions. Furthermore, several transporter genes, oxidoreductases-, and glycosyltransferases-encoding genes were upregulated to effectively sequestrate and detoxify the ADW. This work demonstrates the potential utilization of C. sorokiniana as a tolerant strain for industrial wastewater treatment, emphasizing the regulation of its molecular mechanisms to cope with unfavorable growth conditions.

%B Journal of Hazardous Materials %V 460 %P 132450 %G eng %U https://www.sciencedirect.com/science/article/pii/S0304389423017338 %R https://doi.org/10.1016/j.jhazmat.2023.132450 %0 Journal Article %J Microbiology Spectrum %D 2023 %T Rapid Identification of Pathogens Causing Bloodstream Infections by Raman Spectroscopy and Raman Tweezers %A Katarína Rebrošová %A Silvie Bernatová %A Martin Šiler %A Jan Mašek %A Ota Samek %A Jan Ježek %A Martin Kizovský %A Veronika Holá %A Pavel Zemánek %A Filip Růžička %K BF %K MF %B Microbiology Spectrum %V 11 %P e00028-23 %G eng %U https://journals.asm.org/doi/abs/10.1128/spectrum.00028-23 %R 10.1128/spectrum.00028-23 %0 Journal Article %J Biomed. Opt. Express %D 2023 %T Rapid identification of pathogens in blood serum via Raman tweezers in combination with advanced processing methods %A Ondřej Vaculík %A Silvie Bernatová %A Katarína Rebrošová %A Ota Samek %A Lukáš Šilhan %A Filip Rů žička %A Mojmír Šerý %A Martin Šiler %A Jan Jež ek %A Pavel Zemánek %K AIF %K BF %K LF %K MF %B Biomed. Opt. Express %V 14 %P 6410–6421 %8 Dec %G eng %U https://opg.optica.org/boe/abstract.cfm?URI=boe-14-12-6410 %R 10.1364/BOE.503628 %0 Journal Article %J Journal of Physics: Photonics %D 2023 %T Roadmap for optical tweezers %A Giovanni Volpe %A Onofrio M Maragò %A Halina Rubinsztein-Dunlop %A Giuseppe Pesce %A Alexander B Stilgoe %A Giorgio Volpe %A Georgiy Tkachenko %A Viet Giang Truong %A Síle Nic Chormaic %A Fatemeh Kalantarifard %A Parviz Elahi %A Mikael Käll %A Agnese Callegari %A Manuel I Marqués %A Antonio A R Neves %A Wendel L Moreira %A Adriana Fontes %A Carlos L Cesar %A Rosalba Saija %A Abir Saidi %A Paul Beck %A Jörg S Eismann %A Peter Banzer %A Thales F D Fernandes %A Francesco Pedaci %A Warwick P Bowen %A Rahul Vaippully %A Muruga Lokesh %A Basudev Roy %A Gregor Thalhammer-Thurner %A Monika Ritsch-Marte %A Laura Pérez García %A Alejandro V Arzola %A Isaac Pérez Castillo %A Aykut Argun %A Till M Muenker %A Bart E Vos %A Timo Betz %A Ilaria Cristiani %A Paolo Minzioni %A Peter J Reece %A Fan Wang %A David McGloin %A Justus C Ndukaife %A Romain Quidant %A Reece P Roberts %A Cyril Laplane %A Thomas Volz %A Reuven Gordon %A Dag Hanstorp %A Javier Tello Marmolejo %A Graham D Bruce %A Kishan Dholakia %A Tongcang Li %A Oto Brzobohatý %A Stephen H Simpson %A Pavel Zemánek %A Felix Ritort %A Yael Roichman %A Valeriia Bobkova %A Raphael Wittkowski %A Cornelia Denz %A G V Pavan Kumar %A Antonino Foti %A Maria Grazia Donato %A Pietro G Gucciardi %A Lucia Gardini %A Giulio Bianchi %A Anatolii V Kashchuk %A Marco Capitanio %A Lynn Paterson %A Philip H Jones %A Kirstine Berg-Sørensen %A Younes F Barooji %A Lene B Oddershede %A Pegah Pouladian %A Daryl Preece %A Caroline Beck Adiels %A Anna Chiara De Luca %A Alessandro Magazzù %A David Bronte Ciriza %A Maria Antonia Iatì %A Grover A Swartzlander %K LF %K MF %B Journal of Physics: Photonics %V 5 %P 022501 %8 apr %G eng %U https://dx.doi.org/10.1088/2515-7647/acb57b %R 10.1088/2515-7647/acb57b %0 Journal Article %J Biosensors %D 2023 %T SERS-Tags: Selective Immobilization and Detection of Bacteria by Strain-Specific Antibodies and Surface-Enhanced Raman Scattering %A Benešová, Markéta %A Bernatová, Silvie %A Mika, Filip %A Pokorná, Zuzana %A Ježek, Jan %A Šiler, Martin %A Samek, Ota %A Růžička, Filip %A Rebrošová, Katarína %A Zemánek, Pavel %A Pilát, Zdeněk %K BF %K MF %B Biosensors %V 13 %P 182 %G eng %U https://www.mdpi.com/2079-6374/13/2/182 %R 10.3390/bios13020182 %0 Journal Article %J Surface and Coatings Technology %D 2023 %T Stable a-CSi:H films with a wide range of modulus of elasticity and low internal stress %A Tomas Plichta %A Vaclav Sulc %A Miloslav Ohlidal %A Vladimir Cech %K AIF %K MF %X

Amorphous hydrogenated silicon carbide (a-CSi:H) thin films were deposited by plasma-enhanced chemical vapor deposition using tetravinylsilane as organosilicon precursor. The mechanical properties of the thin films, namely the modulus of elasticity, hardness, and elastic recovery parameter, were determined by nanoindentation, as well as the internal stresses by scanning electron microscopy and optical profilometry. It was found that the modulus of elasticity increased from 10 to 137 GPa with increasing power (2–150 W) delivered to plasma, while the hardness increased from 1.5 to 14.5 GPa. This improvement in mechanical properties with increasing energy delivered to the plasma is related to greater fragmentation of the precursor which led to an increase in the crosslinking of the material network. The compressive internal stresses in the films reached low values of −0.04 to −0.2 GPa with increasing power (2–75 W) and an acceptable −0.5 GPa for 150 W. The elastic recovery parameter decreased with increasing power from 0.86 to 0.64, i.e., the thin films behaved more plasticity with increasing power. The modulus of elasticity and hardness were investigated in terms of the aging of the films for a period of 6 years when samples were stored under ambient conditions. No significant changes in these properties were observed. However, minor changes were observed in the indentation curves obtained for the 2 W and even less for the 10 W samples. Small changes were then also observed for the elastic recovery parameter, whose value for these samples partially decreased which may be related to postdeposition oxidation. No changes in internal stress values over time were observed. The wide range of mechanical properties of stable a-CSi:H films with low internal stress increases their application potential and their wide use as materials with tailored properties from polymer-like to tough material.

%B Surface and Coatings Technology %V 459 %P 129147 %G eng %U https://www.sciencedirect.com/science/article/pii/S0257897222010684 %R https://doi.org/10.1016/j.surfcoat.2022.129147 %0 Journal Article %J Nature Communications %D 2023 %T Synchronization of spin-driven limit cycle oscillators optically levitated in vacuum %A Brzobohatý, Oto %A Duchaň, Martin %A Jákl, Petr %A Ježek, Jan %A Šiler, Martin %A Zemánek, Pavel %A Simpson, Stephen H. %K LF %K MF %B Nature Communications %V 14 %P 5441 %G eng %U https://doi.org/10.1038/s41467-023-41129-5 %R 10.1038/s41467-023-41129-5 %0 Journal Article %J Opt. Lett. %D 2022 %T Absolute frequencies of H13C14N hydrogen cyanide transitions in the 1.5-µm region with the saturated spectroscopy and a sub-kHz scanning laser %A Jan Hrabina %A Martin Hosek %A Simon Rerucha %A Martin Cizek %A Zdenek Pilat %A Massimo Zucco %A Josef Lazar %A Ondrej Cip %K BF %K MF %X

The wide span and high density of lines in its rovibrational spectrum render hydrogen cyanide a useful spectroscopic media for referencing absolute frequencies of lasers in optical communication and dimensional metrology. We determined, for the first time to the best of our knowledge, the molecular transitions' center frequencies of the H13C14N isotope in the range from 1526 nm to 1566 nm with 1.3&\#x00A0;×&\#x00A0;10\textminus10 fractional uncertainty. We investigated the molecular transitions with a highly coherent and widely tunable scanning laser that was precisely referenced to a hydrogen maser through an optical frequency comb. We demonstrated an approach to stabilize the operational conditions needed to maintain the constantly low pressure of the hydrogen cyanide to carry out the saturated spectroscopy with the third-harmonic synchronous demodulation. We demonstrated approximately a forty-fold improvement in the line centers' resolution compared to the previous result.

%B Opt. Lett. %V 47 %P 5704–5707 %8 Nov %G eng %U https://opg.optica.org/ol/abstract.cfm?URI=ol-47-21-5704 %R 10.1364/OL.467633 %0 Journal Article %J Optica %D 2022 %T All-optical sub-Kelvin sympathetic cooling of a levitated microsphere in vacuum %A Y. Arita %A G. D. Bruce %A E. M. Wright %A S. H. Simpson %A P. Zemánek %A K. Dholakia %K LF %K MF %X

We demonstrate all-optical sympathetic cooling of a laser-trapped microsphere to sub-Kelvin temperatures, mediated by optical binding to a feedback-cooled adjacent particle. Our study opens prospects for multi-particle quantum entanglement and sensing in levitated optomechanics.

%B Optica %V 9 %P 1000–1002 %8 Sep %G eng %U https://opg.optica.org/optica/abstract.cfm?URI=optica-9-9-1000 %R 10.1364/OPTICA.466337 %0 Journal Article %J J. Chem. Phys. %D 2022 %T Challenges on optical printing of colloidal nanoparticles %A Violi, Ianina L. %A Martinez, Luciana P. %A Barella, Mariano %A Zaza, Cecilia %A Chvátal, Lukas %A Zemánek, Pavel %A Gutierrez, Marina V. %A Paredes, Maria Y. %A Scarpettini, Alberto F. %A Olmos-Trigo, Jorge %A Pais, Valeria R. %A Noblega, Ivan Diaz %A Cortès, Emiliano %A Saenz, Juan Jose %A Bragas, Andrea V. %A Gargiulo, Juliàn %A Stefani, Fernando D. %K LF %K MF %B J. Chem. Phys. %V 156 %P 034201 %8 JAN 21 %G eng %R 10.1063/5.0078454 %0 Journal Article %J Photonics %D 2022 %T Endoscopic Imaging Using a Multimode Optical Fibre Calibrated with Multiple Internal References %A Jákl, Petr %A Šiler, Martin %A Ježek, Jan %A Cifuentes, Angel %A Trägårdh, Johanna %A Zemánek, Pavel %A Cizmar, Tomas %K BF %K KF %K MF %B Photonics %V 9 %P 37 %G eng %U https://www.mdpi.com/2304-6732/9/1/37 %R 10.3390/photonics9010037 %0 Journal Article %J Proceedings of the Institution of Mechanical Engineers, Part E: Journal of Process Mechanical Engineering %D 2022 %T Experimental analysis of microhardness changes of subsurface areas affected by WEDM %A Katerina Mouralova %A Stefan Michna %A Radim Zahradnicek %A Josef Bednar %A Tomas Plichta %A Jiri Fries %K AIF %K MF %X

The influence of the surface area by the impact of high temperatures after wire electric discharge machining (WEDM) is a known fact. However, the affected parameters also include a change in microhardness. In order to further investigate this statement, 5 different ferrous and non-ferrous materials were selected, from which three samples were always made with different settings of machine parameters (gap voltage, pulse on and off time, wire feed and discharge current). This examined not only the effect of the machining itself on the material but also whether the change in the microhardness of the material is affected by the setting of the machine parameters. In order to measure the microhardness of the subsurface layer, a metallographic preparation was made from each sample, which enabled accurate measurements always in the same area. Subsequent evaluation revealed that the microhardness may not be affected at all and everything depends only on the type of material being machined. The changes in microhardness affected by setting machine parameters are negligible.

%B Proceedings of the Institution of Mechanical Engineers, Part E: Journal of Process Mechanical Engineering %V 236 %P 1979-1991 %G eng %U https://doi.org/10.1177/09544089221078383 %R 10.1177/09544089221078383 %0 Journal Article %J JOURNAL OF APPLIED PHYCOLOGY %D 2022 %T Glycogen, poly(3-hydroxybutyrate) and pigment accumulation in three Synechocystis strains when exposed to a stepwise increasing salt stress %A Meixner, K. %A Daffert, C. %A Dalnodar, D. %A Mrazova, K. %A Hrubanová, K. %A Krzyzanek, V %A Nebesářová, J. %A Samek, O. %A Sedrlova, Z. %A Slaninová, E. %A Sedláček, P. %A Obruča, S. %A Fritz, I %K BF %K MF %B JOURNAL OF APPLIED PHYCOLOGY %V 34 %P 1227-1241 %8 JUN %G eng %R 10.1007/s10811-022-02693-3 %0 Journal Article %J Intelligent Computing %D 2022 %T How to Build the ``Optical Inverse'' of a Multimode Fibre %A Būtaitė, Unė G. %A Kupianskyi, Hlib %A Cizmar, Tomas %A Phillips, David B. %K KF %K MF %B Intelligent Computing %V 2022 %P 9816026 %@ null %G eng %U https://doi.org/10.34133/2022/9816026 %R 10.34133/2022/9816026 %0 Journal Article %J Light: Advanced Manufacturing %D 2022 %T Hybrid multimode - multicore fibre based holographic endoscope for deep-tissue neurophotonics %A Yang Du %A Sergey Turtaev %A Ivo T Leite %A Adrian Lorenz %A Jens Kobelke %A Katrin Wondraczek %A Tomáš Čižmár %K KF %K MF %B Light: Advanced Manufacturing %V 3 %P 1 %G eng %U https://www.light-am.com//article/id/5e7e4e57-462a-4c48-92ca-1aec395fed59 %R 10.37188/lam.2022.029 %0 Journal Article %J SENSORS %D 2022 %T In Vivo Contrast Imaging of Rat Heart with Carbon Dioxide Foam %A Karalko, Anton %A Kesa, Peter %A Jelinek, Frantisek %A Sefc, Ludek %A Ježek, Jan %A Zemánek, Pavel %A Grus, Tomas %K BF %K MF %B SENSORS %V 22 %P 5124 %8 JUL %G eng %R 10.3390/s22145124 %0 Journal Article %J Opt. Express %D 2022 %T A method for single particle tracking through a multimode fiber %A Angel Cifuentes %A Johanna Trägårdh %K KF %K MF %B Opt. Express %V 30 %P 36055–36064 %8 Sep %G eng %U http://opg.optica.org/oe/abstract.cfm?URI=oe-30-20-36055 %R 10.1364/OE.470111 %0 Journal Article %J Opt. Express %D 2022 %T Near perfect focusing through multimode fibres %A André D. Gomes %A Sergey Turtaev %A Yang Du %A Tomáš Čižmár %K KF %K MF %B Opt. Express %V 30 %P 10645–10663 %8 Mar %G eng %U http://opg.optica.org/oe/abstract.cfm?URI=oe-30-7-10645 %R 10.1364/OE.452145 %0 Journal Article %J Neurophotonics %D 2022 %T Neurophotonic tools for microscopic measurements and manipulation: status report %A Ahmed Abdelfattah %A Sapna Ahuja %A Taner Akkin %A Srinivasa Rao Allu %A David A. Boas %A Joshua Brake %A Erin M. Buckley %A Robert E. Campbell %A Anderson I. Chen %A Xiaojun Cheng %A Tomáš Čižmár %A Irene Costantini %A Massimo De Vittorio %A Anna Devor %A Patrick R. Doran %A Mirna El Khatib %A Valentina Emiliani %A Natalie Fomin-Thunemann %A Yeshaiahu Fainman %A Tomás Fernández Alfonso %A Christopher G. L. Ferri %A Ariel Gilad %A Xue Han %A Andrew Harris %A Elizabeth M. C. Hillman %A Ute Hochgeschwender %A Matthew G. Holt %A Na Ji %A Kivilcim Kiliç %A Evelyn M. R. Lake %A Lei Li %A Tianqi Li %A Philipp Mächler %A Rickson C. Mesquita %A Evan W. Miller %A K.M. Naga Srinivas Nadella %A U. Valentin Nägerl %A Yusuke Nasu %A Axel Nimmerjahn %A Petra Ondráčková %A Francesco S. Pavone %A Citlali Perez Campos %A Darcy S. Peterka %A Filippo Pisano %A Ferruccio Pisanello %A Francesca Puppo %A Bernardo L. Sabatini %A Sanaz Sadegh %A Sava Sakadžic %A Shy Shoham %A Sanaya N. Shroff %A R. Angus Silver %A Ruth R. Sims %A Spencer L. Smith %A Vivek J. Srinivasan %A Martin Thunemann %A Lei Tian %A Lin Tian %A Thomas Troxler %A Antoine Valera %A Alipasha Vaziri %A Sergei A. Vinogradov %A Flavia Vitale %A Lihong V. Wang %A Hana Uhlířová %A Chris Xu %A Changhuei Yang %A Mu-Han Yang %A Gary Yellen %A Ofer Yizhar %A Yongxin Zhao %K KF %K MF %B Neurophotonics %V 9 %G eng %U https://doi.org/10.1117/1.NPh.9.S1.013001 %R 10.1117/1.NPh.9.S1.013001 %0 Journal Article %J Spectrochimica Acta Part B: Atomic Spectroscopy %D 2022 %T The potential of combining laser-induced breakdown spectroscopy and Raman spectroscopy data for the analysis of wood samples %A Daniel Holub %A Pavel Pořízka %A Martin Kizovský %A David Prochazka %A Ota Samek %A Josef Kaiser %K BF %K MF %X

We report on combining the surface analysis technique of Laser-induced Breakdown Spectroscopy (LIBS) with Raman spectroscopy. The combination of both techniques enables to study the chemical composition of the sample in a broader context when combining elemental and molecular information. Obtained elemental and molecular spectra are characteristic for individual biological samples (e.g., organs and cells) and are considered as a fingerprint. In this study, Raman spectroscopy is used for the detection of important molecular complexes in selected wood samples, e.g., accurate lignin and cellulose content on distinct spots of the sample surface. We chose Raman as a standard reference technique that is used for the lignin/cellulose ratio estimation. To complement the molecular information, LIBS technique was employed for the imaging of essential nutrients, e.g., Ca, Na, and K. Consequently, the contribution from both analytical techniques was combined and changes in the molecular content were visually correlated to the abundance of nutrition elements and show a direct dependence between the two signal responses. Thus, we can get specific answers to relation of lignin and cellulose formation with nutrients within the plant tissue. This evidence may then be helpful for the study of the effect of various environmental and stress factors.

%B Spectrochimica Acta Part B: Atomic Spectroscopy %V 195 %P 106487 %G eng %U https://www.sciencedirect.com/science/article/pii/S0584854722001318 %R https://doi.org/10.1016/j.sab.2022.106487 %0 Journal Article %J Scientific Reports %D 2022 %T Production of precision slots in copper foil using micro EDM %A Mouralova, Katerina %A Bednar, Josef %A Benes, Libor %A Plichta, Tomáš %A Prokes, Tomas %A Fries, Jiri %K AIF %K MF %B Scientific Reports %V 12 %P 5023 %8 MAR 23 %G eng %R 10.1038/s41598-022-08957-9 %0 Journal Article %J FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY %D 2022 %T Raman Spectroscopy-A Novel Method for Identification and Characterization of Microbes on a Single-Cell Level in Clinical Settings %A Rebrošová, Katarína %A Samek, Ota %A Kizovský, Martin %A Bernatová, Silvie %A Holá, Veronika %A Růžička, Filip %K BF %K MF %B FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY %V 12 %P 866463 %8 APR 22 %G eng %R 10.3389/fcimb.2022.866463 %0 Journal Article %J Analytica Chimica Acta %D 2022 %T Raman spectroscopy—a tool for rapid differentiation among microbes causing urinary tract infections %A Katarína Rebrošová %A Silvie Bernatová %A Martin Šiler %A Magdalena Uhlirova %A Ota Samek %A Jan Ježek %A Veronika Holá %A Filip Růžička %A Pavel Zemánek %K BF %K KF %K MF %B Analytica Chimica Acta %V 1191 %P 339292 %G eng %U https://www.sciencedirect.com/science/article/pii/S0003267021011181 %R https://doi.org/10.1016/j.aca.2021.339292 %0 Journal Article %J Journal of Physics: Photonics %D 2022 %T Roadmap on wavefront shaping and deep imaging in complex media %A Sylvain Gigan %A Ori Katz %A Hilton B de Aguiar %A Esben Ravn Andresen %A Alexandre Aubry %A Jacopo Bertolotti %A Emmanuel Bossy %A Dorian Bouchet %A Joshua Brake %A Sophie Brasselet %A Yaron Bromberg %A Hui Cao %A Thomas Chaigne %A Zhongtao Cheng %A Wonshik Choi %A Tomáš Čižmár %A Meng Cui %A Vincent R Curtis %A Hugo Defienne %A Matthias Hofer %A Ryoichi Horisaki %A Roarke Horstmeyer %A Na Ji %A Aaron K LaViolette %A Jerome Mertz %A Christophe Moser %A Allard P Mosk %A Nicolas C Pégard %A Rafael Piestun %A Sebastien Popoff %A David B Phillips %A Demetri Psaltis %A Babak Rahmani %A Hervé Rigneault %A Stefan Rotter %A Lei Tian %A Ivo M Vellekoop %A Laura Waller %A Lihong Wang %A Timothy Weber %A Sheng Xiao %A Chris Xu %A Alexey Yamilov %A Changhuei Yang %A Hasan Yılmaz %K KF %K MF %X

The last decade has seen the development of a wide set of tools, such as wavefront shaping, computational or fundamental methods, that allow us to understand and control light propagation in a complex medium, such as biological tissues or multimode fibers. A vibrant and diverse community is now working in this field, which has revolutionized the prospect of diffraction-limited imaging at depth in tissues. This roadmap highlights several key aspects of this fast developing field, and some of the challenges and opportunities ahead.

%B Journal of Physics: Photonics %V 4 %P 042501 %8 aug %G eng %U https://dx.doi.org/10.1088/2515-7647/ac76f9 %R 10.1088/2515-7647/ac76f9 %0 Journal Article %J International Journal of Biological Macromolecules %D 2022 %T The role of polyhydroxyalkanoates in adaptation of Cupriavidus necator to osmotic pressure and high concentration of copper ions %A Ivana Novackova %A Vendula Hrabalova %A Eva Slaninova %A Petr Sedlacek %A Ota Samek %A Martin Koller %A Vladislav Krzyzanek %A Kamila Hrubanova %A Katerina Mrazova %A Jana Nebesarova %A Stanislav Obruca %K BF %K MF %X

Polyhydroxyalkanoates (PHA) are abundant microbial polyesters accumulated in the form of intracellular granules by numerous prokaryotes primarily as storage of carbon and energy. Apart from their storage function, the presence of PHA also enhances the robustness of the microbial cells against various stressors. In this work, we investigated the role of PHA in Cupriavidus necator, a model organism concerning PHA metabolism, for adaptation to osmotic pressure and copper ions. In long-term laboratory evolution experiments, the bacterial culture was cultivated in presence of elevated doses of sodium chloride or copper ions (incubations lasted 78 passages for Cu2+ and 68 passages for NaCl) and the evolved strains were compared with the wild-type strain in terms of growth and PHA production capacity, cell morphology (investigated by various electron microscopy techniques), activities of selected enzymes involved in PHA metabolism and other crucial metabolic pathways, the chemical composition of bacterial biomass (determined by infrared and Raman spectroscopy) and also considering robustness against various stressors. The results confirmed the important role of PHA metabolism for adaptation to both tested stressors.

%B International Journal of Biological Macromolecules %V 206 %P 977-989 %G eng %U https://www.sciencedirect.com/science/article/pii/S0141813022005712 %R https://doi.org/10.1016/j.ijbiomac.2022.03.102 %0 Journal Article %J Biomedical Optics Express %D 2022 %T Suppression of the Non-Linear Background in a Multimode Fibre CARS Endoscope %A Pikálek, Tomáš %A Stibůrek, Miroslav %A Simpson, Stephen %A Cizmar, Tomas %A Trägårdh, Johanna %K KF %K MF %B Biomedical Optics Express %V 13 %P 862–864 %G eng %R 10.1364/BOE.450375 %0 Journal Article %J Thin Solid Films %D 2022 %T Surface topography affects the nanoindentation data %A Tomas Plichta %A Radim Zahradnicek %A Vladimir Cech %K AIF %K MF %X

The near-surface mechanical properties of thin films as well as bulk materials are amongst the key parameters important for their application, and instrumented nanoindentation is a standard technique for determining these mechanical properties. However, it is known that the surface topography of the characterized materials may affect the nanoindentation data when a sharp indenter for small penetration depths (displacements) is used. A thin film of hydrogenated amorphous silicon carbide with a thickness of 1.0 μm was deposited on a silicon wafer by plasma-enhanced chemical vapour deposition. The cyclic nanoindentation was used to construct a depth profile of mechanical properties for the flat surface (0.5 nm roughness) of the thin film, which made it possible to determine its modulus of elasticity of 83 GPa and hardness of 8.6 GPa unaffected by the silicon substrate. Grains with a spherical cap geometry with a typical radius of 0.5 µm and a height of 60 nm are distributed along the flat surface of the film. The grains have the same mechanical properties as the deposited film. Depth profiles of mechanical properties were determined for different types of contact between the Berkovich indenter with a radius of 50 nm and the selected grain (grain top, grain foot, two or three grains); i.e. for these measurements the following applied - the radius of the tip curvature was less than grain radii (RBerkovich < Rgrain). Residual imprints after nanoindentation measurements were carefully observed by atomic force microscopy and scanning electron microscopy. The near-surface mechanical properties were significantly affected by the surface topography, and the determined modulus of elasticity and hardness were crucially under- or overestimated in the range of 50% to 100% compared to the real values. The nature of these deviations was discussed. The solution is to use cyclic nanoindentation performed on the flat surfaces or on the top of grains, followed by extrapolation of the depth profiles to the zero-contact depth (film surface).

%B Thin Solid Films %V 745 %P 139105 %G eng %U https://www.sciencedirect.com/science/article/pii/S0040609022000268 %R https://doi.org/10.1016/j.tsf.2022.139105 %0 Journal Article %J Polymers %D 2021 %T The Adhesion of Plasma Nanocoatings Controls the Shear Properties of GF/Polyester Composite %A Plichta, Tomáš %A Širjovová, Veronika %A Zvonek, Milan %A Kalinka, Gerhard %A Čech, Vladimír %K AIF %K MF %X

High-performance fibre-reinforced polymer composites are important construction materials based not only on the specific properties of the reinforcing fibres and the flexible polymer matrix but also on the compatible properties of the composite interphase. First, oxygen-free (a-CSi:H) and oxygen-binding (a-CSiO:H) plasma nanocoatings of different mechanical and tribological properties were deposited on planar silicon dioxide substrates that closely mimic E-glass. The nanoscratch test was used to characterize the nanocoating adhesion expressed in terms of critical normal load and work of adhesion. Next, the same nanocoatings were deposited on E-glass fibres, which were used as reinforcements in the polyester composite to affect its interphase properties. The shear properties of the polymer composite were characterized by macro- and micromechanical tests, namely a short beam shear test to determine the short-beam strength and a single fibre push-out test to determine the interfacial shear strength. The results of the polymer composites showed a strong correlation between the short-beam strength and the interfacial shear strength, proving that both tests are sensitive to changes in fibre-matrix adhesion due to different surface modifications of glass fibres (GF). Finally, a strong correlation between the shear properties of the GF/polyester composite and the adhesion of the plasma nanocoating expressed through the work of adhesion was demonstrated. Thus, increasing the work of adhesion of plasma nanocoatings from 0.8 to 1.5 mJ·m−2 increased the short-beam strength from 23.1 to 45.2 MPa. The results confirmed that the work of adhesion is a more suitable parameter in characterising the level of nanocoating adhesion in comparison with the critical normal load.

%B Polymers %V 13 %P 593 %G eng %U https://www.mdpi.com/2073-4360/13/4/593 %R 10.3390/polym13040593 %0 Journal Article %J Chemical Engineering Journal %D 2021 %T An aerogel-based photocatalytic microreactor driven by light guiding for degradation of toxic pollutants %A Ozbakir, Yaprak %A Jonas, Alexandr %A Kiraz, Alper %A Erkey, Can %K LF %K MF %B Chemical Engineering Journal %V 409 %P 128108 %8 APR 1 %G eng %R 10.1016/j.cej.2020.128108 %0 Journal Article %J Opt. Express %D 2021 %T All-optical manipulation of photonic membranes %A Meisam Askari %A Blair C. Kirkpatrick %A Tomáš Čižmár %A Andrea Di Falco %K KF %K MF %X

We demonstrate the all-optical manipulation of polymeric membranes in microfluidic environments. The membranes are decorated with handles for their use in holographic optical tweezers systems. Our results show that due to their form factor the membranes present a substantial increase in their mechanical stability, respect to micrometric dielectric particles. This intrinsic superior stability is expected to improve profoundly a wide range of bio-photonic applications that rely on the optical manipulation of micrometric objects.

%B Opt. Express %V 29 %P 14260–14268 %8 May %G eng %U http://www.opticsexpress.org/abstract.cfm?URI=oe-29-10-14260 %R 10.1364/OE.420364 %0 Journal Article %J LIGHT-SCIENCE & APPLICATIONS %D 2021 %T Compressively sampling the optical transmission matrix of a multimode fibre %A Li, Shuhui %A Saunders, Charles %A Lum, Daniel J. %A Murray-Bruce, John %A Goyal, Vivek K. %A Cizmar, Tomas %A Phillips, David B. %K KF %K MF %B LIGHT-SCIENCE & APPLICATIONS %V 10 %P 88 %8 APR 21 %G eng %R 10.1038/s41377-021-00514-9 %0 Journal Article %J Opt. Express %D 2021 %T Computational image enhancement of multimode fibre-based holographic endo-microscopy: harnessing the muddy modes %A Tereza Tučková %A Martin Šiler %A DE Boonzajer Flaes %A Petr Jákl %A Sergey Turtaev %A Stanislav Krátký %A Rainer Heintzmann %A Hana Uhlířová %A Tomáš Čižmár %K KF %K MF %B Opt. Express %V 29 %P 38206–38220 %8 Nov %G eng %U http://www.osapublishing.org/oe/abstract.cfm?URI=oe-29-23-38206 %R 10.1364/OE.434848 %0 Journal Article %J Nature Communications %D 2021 %T Memory effect assisted imaging through multimode optical fibres %A Li, Shuhui %A Horsley, Simon A. R. %A Tyc, Tomáš %A Cizmar, Tomas %A Phillips, David B. %K KF %K MF %X

When light propagates through opaque material, the spatial information it holds becomes scrambled, but not necessarily lost. Two classes of techniques have emerged to recover this information: methods relying on optical memory effects, and transmission matrix (TM) approaches. Here we develop a general framework describing the nature of memory effects in structures of arbitrary geometry. We show how this framework, when combined with wavefront shaping driven by feedback from a guide-star, enables estimation of the TM of any such system. This highlights that guide-star assisted imaging is possible regardless of the type of memory effect a scatterer exhibits. We apply this concept to multimode fibres (MMFs) and identify a `quasi-radial' memory effect. This allows the TM of an MMF to be approximated from only one end - an important step for micro-endoscopy. Our work broadens the applications of memory effects to a range of novel imaging and optical communication scenarios.

%B Nature Communications %V 12 %P 3751 %G eng %U https://doi.org/10.1038/s41467-021-23729-1 %R 10.1038/s41467-021-23729-1 %0 Journal Article %J APL Photonics %D 2021 %T Observing distant objects with a multimode fiber-based holographic endoscope %A Leite,Ivo T. %A Turtaev,Sergey %A Boonzajer Flaes,Dirk E. %A Čižmár,Tomáš %K KF %K MF %B APL Photonics %V 6 %P 036112 %G eng %U https://doi.org/10.1063/5.0038367 %R 10.1063/5.0038367 %0 Journal Article %J ACS Applied Materials & Interfaces %D 2021 %T Optically transportable optofluidic microlasers with liquid crystal cavities tuned by the electric field %A Jonas, Alexandr %A Pilát, Zdeněk %A Ježek, Jan %A Bernatová, Silvie %A Jedlička, Petr %A Aas, Mehdi %A Kiraz, Alper %A Zemánek, Pavel %K BF %K LF %K MF %B ACS Applied Materials & Interfaces %V 13 %P 50657−50667 %8 OCT 21 %G eng %R 10.1021/acsami.1c11936 %0 Journal Article %J Optica %D 2021 %T Polarization-resolved second-harmonic generation imaging through a multimode fiber %A Cifuentes, Angel %A Pikálek, Tomáš %A Ondráčková, Petra %A Amezcua-Correa, Rodrigo %A Antonio-Lopez, José Enrique %A Cizmar, Tomas %A Trägårdh, Johanna %K KF %K MF %B Optica %V 8 %P 1065–1074 %G eng %0 Journal Article %J NANOPHOTONICS %D 2021 %T The potential of SERS as an AST methodology in clinical settings %A Samek, Ota %A Bernatová, Silvie %A Dohnal, Fadi %K BF %K MF %B NANOPHOTONICS %V 10 %P 2537-2561 %8 AUG %G eng %R 10.1515/nanoph-2021-0095 %0 Journal Article %J Biosensors %D 2021 %T Raman Microspectroscopic Analysis of Selenium Bioaccumulation by Green Alga Chlorella vulgaris %A Kizovský, Martin %A Pilát, Zdeněk %A Mylenko, Mykola %A Hrouzek, Pavel %A Kuta, Jan %A Skoupý, Radim %A Krzyžánek, Vladislav %A Hrubanová, Kamila %A Adamczyk, Olga %A Ježek, Jan %A Bernatová, Silvie %A Klementová, Tereza %A Gjevik, Alžběta %A Šiler, Martin %A Samek, Ota %A Zemánek, Pavel %K BF %K MF %B Biosensors %V 11 %P 115 %G eng %U https://www.mdpi.com/2079-6374/11/4/115 %R 10.3390/bios11040115 %0 Journal Article %J Eur. Phys. J. Plus %D 2021 %T Rapid detection of antibiotic sensitivity of Staphylococcus aureus by Raman tweezers %A Bernatová, S. %A K. Rebrošová %A Pilát, Z. %A M. Šerý %A Gjevik, A. %A Samek, O. %A Ježek, J. %A Šiler, M. %A Kizovský, M. %A Klementová, T. %A Holá, V. %A F. Růžička %A Zemánek, P. %K BF %K KF %K MF %B Eur. Phys. J. Plus %V 136 %P 233 %G eng %U https://doi.org/10.1140/epjp/s13360-021-01152-1 %R 10.1140/epjp/s13360-021-01152-1 %0 Journal Article %J Opt. Express %D 2021 %T Side-view holographic endomicroscopy via a custom-terminated multimode fibre %A Beatriz M. Silveira %A Tomáš Pikálek %A Miroslav Stibůrek %A Petra Ondráčková %A Petr Jákl %A Ivo T. Leite %A Tomáš Čižmár %K KF %K MF %X

Microendoscopes based on optical fibres have recently come to the fore as promising candidates allowing in-vivo observations of otherwise inaccessible biological structures in animal models. Despite being still in its infancy, imaging can now be performed at the tip of a single multimode fibre, by relying on powerful holographic methods for light control. Fibre based endoscopy is commonly performed en face, resulting in possible damage of the specimen owing to the direct contact between the distal end of the probe and target. On this ground, we designed an all-fibre probe with an engineered termination that reduces compression and damage to the tissue under investigation upon probe insertion. The geometry of the termination brings the field of view to a plane parallel to the fibre&\#x2019;s longitudinal direction, conveying the probe with off-axis imaging capabilities. We show that its focusing ability also benefits from a higher numerical aperture, resulting in imaging with increased spatial resolution. The effect of probe insertion was investigated inside a tissue phantom comprising fluorescent particles suspended in agarose gel, and a comparison was established between the novel side-view probe and the standard en face fibre probe. This new concept paves the way to significantly less invasive deep-tissue imaging.

%B Opt. Express %V 29 %P 23083–23095 %G eng %U http://www.osapublishing.org/oe/abstract.cfm?URI=oe-29-15-23083 %R 10.1364/OE.426235 %0 Journal Article %J Optica %D 2021 %T Stochastic dynamics of optically bound matter levitated in vacuum %A Vojtech Svak %A Jana Flajšmanová %A Lukáš Chvátal %A Martin Šiler %A Alexandr Jonáš %A Jan Ježek %A Stephen H. Simpson %A Pavel Zemánek %A Oto Brzobohatý %K LF %K MF %B Optica %V 8 %P 220–229 %8 Feb %G eng %R 10.1364/OPTICA.404851 %0 Journal Article %J Phys. Rev. A %D 2021 %T Stochastic Hopf bifurcations in vacuum optical tweezers %A Simpson, Stephen H. %A Arita, Yoshihiko %A Dholakia, Kishan %A Zemánek, Pavel %K LF %K MF %B Phys. Rev. A %V 104 %P 043518 %8 OCT 15 %G eng %R 10.1103/PhysRevA.104.043518 %0 Journal Article %J Opt. Express %D 2021 %T Thermal stability of wavefront shaping using a DMD as a spatial light modulator %A Benjamin Rudolf %A Yang Du %A Sergey Turtaev %A Ivo T. Leite %A Tomáš Čižmár %K KF %K MF %B Opt. Express %V 29 %P 41808–41818 %8 Dec %G eng %U http://www.osapublishing.org/oe/abstract.cfm?URI=oe-29-25-41808 %R 10.1364/OE.442284 %0 Journal Article %J Opt. Express %D 2021 %T Time-averaged image projection through a multimode fiber %A Dirk Boonzajer Flaes %A Hana Štolzová %A Tomáš Čižmár %K KF %K MF %X

Many disciplines, ranging from lithography to opto-genetics, require high-fidelity image projection. However, not all optical systems can display all types of images with equal ease. Therefore, the image projection quality is dependent on the type of image. In some circumstances, this can lead to a catastrophic loss of intensity or image quality. For complex optical systems, it may not be known in advance which types of images pose a problem. Here we show a new method called Time-Averaged image Projection (TAP), allowing us to mitigate these limitations by taking the entire image projection system into account despite its complexity and building the desired intensity distribution up from multiple illumination patterns. Using a complex optical setup, consisting of a wavefront shaper and a multimode optical fiber illuminated by coherent light, we succeeded to suppress any speckle-related background. Further, we can display independent images at multiple distances simultaneously, and alter the effective sharpness depth through the algorithm. Our results demonstrate that TAP can significantly enhance the image projection quality in multiple ways. We anticipate that our results will greatly complement any application in which the response to light irradiation is relatively slow (one microsecond with current technology) and where high-fidelity spatial distribution of optical power is required.

%B Opt. Express %V 29 %P 28005–28020 %G eng %U http://www.osapublishing.org/oe/abstract.cfm?URI=oe-29-18-28005 %R 10.1364/OE.431842 %0 Journal Article %J Science %D 2021 %T Time-of-flight 3D imaging through multimode optical fibers %A Daan Stellinga %A David B. Phillips %A Simon Peter Mekhail %A Adam Selyem %A Sergey Turtaev %A Tomáš Čižmár %A Miles J. Padgett %K KF %K MF %B Science %V 374 %P 1395-1399 %G eng %R 10.1126/science.abl3771 URL = https://www.science.org/doi/abs/10.1126/science.abl3771 %0 Journal Article %J The European Physical Journal - Plus %D 2021 %T T-matrix calculations of spin-dependent optical forces in optically trapped nanowires %A Polimeno, P. %A Iati, M. A. %A Boschi, C. Degli Esposti %A Simpson, S. H. %A Svak, V. %A Brzobohatý, O. %A Zemánek, P. %A Marago, O. M. %A Saija, R. %K LF %K MF %B The European Physical Journal - Plus %V 136 %P 86 %8 JAN 16 %G eng %R 10.1140/epjp/s13360-020-01057-5 %0 Journal Article %J Microorganisms %D 2021 %T The Use of Raman Spectroscopy to Monitor Metabolic Changes in Stressed Metschnikowia sp. Yeasts %A Němcová, Andrea %A Gonová, Dominika %A Samek, Ota %A Sipiczki, Matthias %A Breierová, Emilia %A Márová, Ivana %K BF %K MF %X

Raman spectroscopy is a universal method designed for the analysis of a wide range of physical, chemical and biological systems or various surfaces. This technique is suitable to monitor various components of cells, tissues or microorganisms. The advantages include very fast non-contact and non-destructive analysis and no or minimal need for sample treatment. The yeasts Metschnikowia can be considered as industrially usable producers of pulcherrimin or single-cell lipids, depending on cultivation conditions and external stress. In the present study, Raman spectroscopy was used as an effective tool to identify both pulcherrimin and lipids in single yeast cells. The analysis of pulcherrimin is very demanding; so far, there is no optimal procedure to analyze or identify this pigment. Based on results, the strong dependence of pulcherrimin production on the ferric ion concentration was found with the highest yield in media containing 0.1 g/L iron. Further, production of lipids in Metschnikowia cells was studied at different temperatures and C:N ratios, using Raman spectroscopy to follow fatty acids composition, under different regimes, by monitoring the iodine number. The results of Raman spectroscopy were comparable with the fatty acid analysis obtained by gas chromatography. This study therefore supported use of Raman spectroscopy for biotechnological applications as a simple tool in the identification and analysis both the pulcherrimin and microbial lipids. This method provides a quick and relatively accurate estimation of targeted metabolites with minimal sample modification and allows to monitor metabolic changes over time of cultivation.

%B Microorganisms %V 9 %P 277 %G eng %U https://www.mdpi.com/2076-2607/9/2/277 %R 10.3390/microorganisms9020277 %0 Journal Article %J Microorganisms %D 2021 %T Use of Waste Substrates for the Lipid Production by Yeasts of the Genus Metschnikowia—Screening Study %A Němcová, Andrea %A Szotkowski, Martin %A Samek, Ota %A Cagáňová, Linda %A Sipiczki, Matthias %A Márová, Ivana %K BF %K MF %X

Oleogenic yeasts are characterized by the ability to accumulate increased amounts of lipids under certain conditions. These microbial lipids differ in their fatty acid composition, which allows them to be widely used in the biotechnology industry. The interest of biotechnologists is closely linked to the rising prices of fossil fuels in recent years. Their negative environmental impact is caused by significantly increased demand for biodiesel. The composition of microbial lipids is very similar to vegetable oils, which provides great potential for use in the production of biodiesel. In addition, some oleogenic microorganisms are capable of producing lipids with a high proportion of unsaturated fatty acids. The presented paper’s main aim was to study the production of lipids and lipid substances by yeasts of the genus Metschnikowia, to cultivate crude waste animal fat to study its utilization by yeasts, and to apply the idea of circular economy in the biotechnology of Metschnikowia yeasts. The work focuses on the influence of various stress factors in the cultivation process, such as reduced temperature or nutritional stress through the use of various waste substrates, together with manipulating the ratio of carbon and nitrogen sources in the medium. Yeast production properties were monitored by several instrumental techniques, including gas chromatography and Raman spectroscopy. The amount of lipids and in particular the fatty acid composition varied depending on the strains studied and the culture conditions used. The ability of yeast to produce significant amounts of unsaturated fatty acids was also demonstrated in the work. The most suitable substrate for lipid production was a medium containing glycerol, where the amount of accumulated lipids in the yeast M. pulcherrima 1232 was up to 36%. In our work, the crude animal fat was used for the production of high-value lipids, which to the best of our knowledge is a new result. Moreover, quantitative screening of lipase enzyme activity cultivated on animal fat substrate on selected yeasts of the genus Metschnikowia was performed. We found that for the yeast utilizing glycerol, animal fat seems to be an excellent source of carbon. Therefore, the yeast conversion of crude processed animal fat to value-added products is a valuable process for the biotechnology and food industry.

%B Microorganisms %V 9 %P 2295 %G eng %U https://www.mdpi.com/2076-2607/9/11/2295 %R 10.3390/microorganisms9112295 %0 Journal Article %J Analytical Chemistry %D 2020 %T Analysis of bacteriophage-host interaction by Raman tweezers %A Pilát, Z %A Jonáš, A %A Pilátová, J %A Klementová, T %A Bernatová, S %A Šiler, M %A Maňka, T %A Kizovský, M %A Růžička, F %A Panůček, R %A Neugebauer, U %A Samek, O %A Zemánek, P %K BF %K KF %K MF %B Analytical Chemistry %V 92 %P 12304–12311 %G eng %0 Journal Article %J Nature %D 2020 %T Cellular locomotion using environmental topography %A Anne Reversat %A Florian Gaertner %A Jack Merrin %A Julian Stopp %A Saren Tasciyan %A Juan Aguilera %A Ingrid de Vries %A Robert Hauschild %A Miroslav Hons %A Matthieu Piel %A Andrew Callan-Jones %A Raphael Voituriez %A Michael Sixt %K KF %K MF %B Nature %V 582 %P 582–585 %G eng %0 Journal Article %J Science Advances %D 2020 %T Coherent oscillations of a levitated birefringent microsphere in vacuum driven by nonconservative rotation-translation coupling %A Arita, Y %A Simpson, SH %A Zemánek, P %A Dholakia, K %K LF %K MF %B Science Advances %V 6 %G eng %0 Journal Article %J Opt. Express %D 2020 %T Complex colloidal structures with non-linear optical properties formed in an optical trap %A Oto Brzobohatý %A Lukáš Chvátal %A Martin Šiler %A Pavel Zemánek %K LF %K MF %B Opt. Express %V 28 %P 37700–37707 %G eng %0 Journal Article %J Frontiers in Physics %D 2020 %T Entropy Production in an Elementary, Light Driven Micro-Machine %A Box, Stuart J. %A Allen, Michael P. %A Phillips, David B. %A Simpson, Stephen H. %K KF %K LF %K MF %X

We consider the basic, thermodynamic properties of an elementary micro-machine operating at colloidal length scales. In particular, we track and analyze the driven stochastic motion of a carefully designed micro-propeller rotating unevenly in an optical tweezers, in water. In this intermediate regime, the second law of macroscopic thermodynamics is satisfied only as an ensemble average, and individual trajectories can be temporarily associated with decreases in entropy. We show that our light driven micro-propeller satisfies an appropriate fluctuation theorem that constrains the probability with which these apparent violations of the second law occur. Implications for the development of more complex micro-machines are discussed.

%B Frontiers in Physics %V 8 %P 538 %G eng %U https://www.frontiersin.org/article/10.3389/fphy.2020.593122 %R 10.3389/fphy.2020.593122 %0 Journal Article %J Advanced Science %D 2020 %T Nanovortex-driven all-dielectric optical diffusion boosting and sorting concept for lab-on-a-chip platforms %A Valero, AC %A Kislov, D %A Gurvitz, EA %A Shamkhi, HK %A Pavlov, AA %A Redka, D %A Yankin, S %A Zemánek, P %A Shalin, AS %K LF %K MF %B Advanced Science %V 7 %G eng %R 10.1002/advs.201903049 %0 Journal Article %J Analytical Chemistry %D 2020 %T Size-based sorting of emulsion droplets in microfluidic channels patterned with laser-ablated guiding tracks %A Rehman, AU %A Coskun, UC %A Rashid, Z %A Morova, B %A Jonáš, A %A Erten, A %A Kiraz, A %K LF %K MF %B Analytical Chemistry %V 92 %P 2597–2604 %G eng %0 Journal Article %J Scientific Reports %D 2020 %T Using the transient trajectories of an optically levitated nanoparticle to characterize a stochastic Duffing oscillator %A Flajšmanová, Jana %A Šiler, Martin %A Jedlička, Petr %A Hrubý, František %A Brzobohatý, Oto %A Filip, Radim %A Zemánek, Pavel %K LF %K MF %B Scientific Reports %V 10 %P 14436 %G eng %0 Journal Article %J Anal. Chem. %D 2019 %T Controlled Oil/Water Partitioning of Hydrophobic Substrates Extending the Bioanalytical Applications of Droplet-Based Microfluidics %A Buryška, T. %A Vašina, M. %A Gielen, F. %A Vaňáček, P. %A van Vliet, L. %A Ježek, J. %A Pilát, Z. %A Zemánek, P. %A Damborský, J. %A Hollfelder, F. %A Prokop, Z. %K BF %K MF %B Anal. Chem. %V 91 %P 10008-10015 %G eng %R 10.1021/acs.analchem.9b01839 %0 Journal Article %J Europ. J. of Pharmaceutical Sci. %D 2019 %T The effects of the treatment conditions on the dissolution profile of ethylcellulose coated pellets %A Pavloková, S. %A Mušelík, J. %A Sabadková, D. %A Bernatová, S. %A Samek, O. %A Neumann, D. %A Franc, A. %K BF %K MF %B Europ. J. of Pharmaceutical Sci. %V 132 %P 86-95 %G eng %R 10.1016/j.ejps.2019.02.034 %0 Journal Article %J Future Microbiology %D 2019 %T Identification of ability to form biofilm in Candida parapsilosis and Staphylococcus epidermidis by Raman spectroscopy %A Rebrošová, Katarína %A Šiler, Martin %A Samek, Ota %A Růžička, Filip %A Bernatová, Silvie %A Ježek, Jan %A Zemánek, Pavel %A Holá, Veronika %K BF %K KF %K MF %X

Aim: Finding rapid, reliable diagnostic methods is a big challenge in clinical microbiology. Raman spectroscopy is an optical method used for multiple applications in scientific fields including microbiology. This work reports its potential in identifying biofilm positive strains of Candida parapsilosis and Staphylococcus epidermidis. Materials & methods: We tested 54 S. epidermidis strains (23 biofilm positive, 31 negative) and 51 C. parapsilosis strains (27 biofilm positive, 24 negative) from colonies on Mueller-Hinton agar plates, using Raman spectroscopy. Results: The accuracy was 98.9% for C. parapsilosis and 96.1% for S. epidermidis. Conclusion: The method showed great potential for identifying biofilm positive bacterial and yeast strains. We suggest that Raman spectroscopy might become a useful aid in clinical diagnostics.

%B Future Microbiology %V 14 %P 509-517 %G eng %U https://doi.org/10.2217/fmb-2018-0297 %R 10.2217/fmb-2018-0297 %0 Journal Article %J Opt. Express %D 2019 %T Label-free CARS microscopy through a multimode fiber endoscope %A Johanna Trägårdh %A Tomáš Pikálek %A Mojmír Šerý %A Tobias Meyer %A Jürgen Popp %A Tomáš Čižmár %K KF %K MF %X

Multimode fibres have recently been employed as high-resolution ultra-thin endoscopes, capable of imaging biological structures deep inside tissue in vivo. Here, we extend this technique to label-free non-linear microscopy with chemical contrast using coherent anti-Stokes Raman scattering (CARS) through a multimode fibre endoscope, which opens up new avenues for instant and in-situ diagnosis of potentially malignant tissue. We use a commercial 125 &\#x00B5;m diameter, 0.29 NA GRIN fibre, and wavefront shaping on an SLM is used to create foci that are scanned behind the fibre facet across the sample. The chemical selectivity is demonstrated by imaging 2 &\#x00B5;m polystyrene and 2.5 &\#x00B5;m PMMA beads with per pixel integration time as low as 1 ms for epi-detection.

%B Opt. Express %V 27 %P 30055–30066 %G eng %U http://www.opticsexpress.org/abstract.cfm?URI=oe-27-21-30055 %R 10.1364/OE.27.030055 %0 Journal Article %J LANGMUIR %D 2019 %T Mechanical Contact Spectroscopy: Characterizing Nanoscale Adhesive Contacts via Thermal Forces %A Jonas, Alexandr %A Kochanczyk, Martin %A Ramirez, Alexandro D. %A Speidel, Michael %A Florin, Ernst-Ludwig %K LF %K MF %B LANGMUIR %V 35 %P 5809-5820 %8 APR 30 %G eng %R 10.1021/acs.langmuir.8b04074 %0 Journal Article %J Opt. Express %D 2019 %T Nanobore fiber focus trap with enhanced tuning capabilities %A Malte Plidschun %A Stefan Weidlich %A Martin Šiler %A Karina Weber %A Tomáš Čižmár %A Markus A. Schmidt %K KF %K MF %B Opt. Express %V 27 %P 36221–36230 %8 Dec %G eng %U http://www.opticsexpress.org/abstract.cfm?URI=oe-27-25-36221 %R 10.1364/OE.27.036221 %0 Journal Article %J Nano Lett. %D 2019 %T Optical Trapping, Optical Binding, and Rotational Dynamics of Silicon Nanowires in Counter-Propagating Beams %A Donato, Maria G. %A Oto Brzobohatý %A S. H. Simpson %A Irrera, Alessia %A Leonardi, Antonio A. %A Lo Faro, Maria J. %A Vojtech Svak %A Maragò, Onofrio M. %A P. Zemánek %K LF %K MF %B Nano Lett. %V 19 %P 342-352 %G eng %R 10.1021/acs.nanolett.8b03978 %0 Journal Article %J Opt. Lett. %D 2019 %T Optomechanical properties of optically self-arranged colloidal waveguides %A Oto Brzobohatý %A Lukáš Chvátal %A P. Zemánek %K LF %K MF %B Opt. Lett. %V 44 %P 707-710 %G eng %R 10.1364/OL.44.000707 %0 Journal Article %J MICROFLUIDICS AND NANOFLUIDICS %D 2019 %T Passive sorting of emulsion droplets with different interfacial properties using laser-patterned surfaces %A Rashid, Zeeshan %A Erten, Ahmet %A Morova, Berna %A Muradoglu, Metin %A Jonas, Alexandr %A Kiraz, Alper %K LF %K MF %B MICROFLUIDICS AND NANOFLUIDICS %V 23 %P 65 %8 MAY %G eng %R 10.1007/s10404-019-2236-8 %0 Journal Article %J Adv. Opt. Photon. %D 2019 %T Perspective on light-induced transport of particles: from optical forces to phoretic motion %A Pavel Zemánek %A Giorgio Volpe %A Alexandr Jonáš %A Oto Brzobohatý %K LF %K MF %B Adv. Opt. Photon. %V 11 %P 577–678 %8 Sep %G eng %U http://aop.osa.org/abstract.cfm?URI=aop-11-3-577 %R 10.1364/AOP.11.000577 %0 Journal Article %J Sci. Rep. %D 2019 %T Spin to orbital light momentum conversion visualized by particle trajectory %A Alejandro V. Arzola %A Lukáš Chvátal %A P Jákl %A P. Zemánek %K LF %K MF %B Sci. Rep. %V 9 %P 4127:1-7 %G eng %R 10.1038/s41598-019-40475-z %0 Journal Article %J ACS Phot. %D 2019 %T Tunable Soft-Matter Optofluidic Waveguides Assembled by Light %A Oto Brzobohatý %A Lukáš Chvátal %A A. Jonáš %A M Šiler %A J. Kaňka %A J Ježek %A P. Zemánek %K LF %K MF %B ACS Phot. %V 6 %P 403-410 %G eng %R 10.1021/acsphotonics.8b01331 %0 Journal Article %J Physical Review D %D 2019 %T Visualizing gravitational Bessel waves %A Paták, Aleš %A Zouhar, Martin %A Řiháček, Tomáš %A Brzobohatý, Oto %A Geršl, Jan %A Campbell, Anna Charvátová %K LF %K MF %B Physical Review D %V 100 %P 044050 %G eng %0 Journal Article %J Opt. Express %D 2019 %T Wavelength dependent characterization of a multimode fibre endoscope %A Tomáš Pikálek %A Johanna Trägårdh %A Stephen Simpson %A Tomáš Čižmár %K KF %K MF %X

Multimode fibres have recently shown promise as miniature endoscopic probes. When used for non-linear microscopy, the bandwidth of the imaging system limits the ability to focus light from broadband pulsed lasers as well as the possibility of wavelength tuning during the imaging. We demonstrate that the bandwidth is limited by the dispersion of the off-axis hologram displayed on the SLM, which can be corrected for, and by the limited bandwidth of the fibre itself. The selection of the fibre is therefore crucial for these experiments. In addition, we show that a standard prism pulse compressor is sufficient for material dispersion compensation for multi-photon imaging with a fibre endoscope.

%B Opt. Express %V 27 %P 28239–28253 %G eng %U http://www.opticsexpress.org/abstract.cfm?URI=oe-27-20-28239 %R 10.1364/OE.27.028239 %0 Journal Article %J J. Phys. Chem. C %D 2019 %T Wavelength-Dependent Optical Force Aggregation of Gold Nanorods for SERS in a Microfluidic Chip %A Bernatová, Silvie %A Donato, Maria Grazia %A Ježek, Jan %A Pilát, Z. %A Samek, Ota %A Magazzu, Alessandro %A Maragò, Onofrio M. %A Zemánek, Pavel %A Gucciardi, Pietro G. %K BF %K MF %B J. Phys. Chem. C %V 123 %P 5608-5615 %G eng %R 10.1021/acs.jpcc.8b12493 %0 Journal Article %J Appl. Microbiol. Biotech. %D 2019 %T What keeps polyhydroxyalkanoates in bacterial cells amorphous? A derivation from stress exposure experiments %A P. Sedláček %A Slaninová, E. %A Enev, V. %A Koller, M. %A J. Nebesářová %A I. Márová %A K. Hrubanová %A V. Krzyžánek %A O. Samek %A S. Obruča %K BF %K MF %B Appl. Microbiol. Biotech. %V 103 %P 1905-1917 %G eng %R 10.1007/s00253-018-09584-z %0 Journal Article %J Spec. Acta Part B %D 2018 %T Combination of laser-induced breakdown spectroscopy and Raman spectroscopy for multivariate classification of bacteria %A D. Procházka %A M. Mazura %A O. Samek %A K. Rebrošová %A P. Pořízka %A J. Klus %A P. Procházková %A J. Novotný %A K. Novotný %A J. Kaiser %K BF %K MF %B Spec. Acta Part B %V 139 %P 6-12 %G eng %R 10.1016/j.sab.2017.11.004 %0 Journal Article %J Sensors %D 2018 %T Detection of chloroalkanes by surface-enhanced raman spectroscopy in microfluidic chips %A Z. Pilát %A Kizovský, M. %A J Ježek %A Krátký, S. %A Sobota, J. %A M Šiler %A O. Samek %A Buryška, T. %A Vaňáček, P. %A Damborský, J. %A Prokop, Z. %A P. Zemánek %K BF %K MF %B Sensors %V 18 %P 3212 %G eng %R 10.3390/s18103212 %0 Journal Article %J Phys. Rev. Lett. %D 2018 %T Diffusing up the Hill: Dynamics and Equipartition in Highly Unstable Systems %A M Šiler %A Ornigotti, L. %A Oto Brzobohatý %A P Jákl %A Artem Ryabov %A Holubec, V. %A P. Zemánek %A Radim Filip %K LF %K MF %B Phys. Rev. Lett. %V 121 %P 23601 %G eng %R 10.1103/PhysRevLett.121.230601 %0 Journal Article %J Light: Sci. Appl. %D 2018 %T Enhancement of the `tractor-beam' pulling force on an optically bound structure %A Damková, Jana %A Lukáš Chvátal %A J Ježek %A Oulehla, Jindrich %A Oto Brzobohatý %A P. Zemánek %K LF %K MF %B Light: Sci. Appl. %V 7 %P 17135 %G eng %R 10.1038/lsa.2017.135 %0 Journal Article %J Light: Sci. Appl. %D 2018 %T High-fidelity multimode fibre-based endoscopy for deep brain in vivo imaging %A S. Turtaev %A I.T. Leite %A Altwegg-Boussac, T. %A Pakan, J.M.P. %A Rochefort, N.L. %A Tomáš Čižmár %K KF %K MF %B Light: Sci. Appl. %V 7 %P 92 %G eng %R 10.1038/s41377-018-0094-x %0 Journal Article %J Sensors %D 2018 %T Microfluidic Cultivation and Laser Tweezers Raman Spectroscopy of E-coli under Antibiotic Stress %A Z. Pilát %A Silva Bernatová %A J Ježek %A Kirchhoff, J. %A Tannert, A. %A Neugebauer, U. %A O. Samek %A P. Zemánek %K BF %K MF %B Sensors %V 18 %P 1623 %G eng %R 10.3390/s18051623 %0 Journal Article %J Sensors %D 2018 %T Monitoring Candida parapsilosis and Staphylococcus epidermidis Biofilms by a Combination of Scanning Electron Microscopy and Raman Spectroscopy %A K. Hrubanová %A V. Krzyžánek %A J. Nebesářová %A F. Růžička %A Z. Pilát %A O. Samek %K BF %K MF %B Sensors %V 18 %P 4089 %G eng %R 10.3390/s18124089 %0 Journal Article %J Royal Society Open Science %D 2018 %T A new type of microphotoreactor with integrated optofluidic waveguide based on solid-air nanoporous aerogels %A Ozbakir, Y. %A A. Jonáš %A Alper Kiraz %A Erkey, C. %K BF %K MF %B Royal Society Open Science %V 5 %P 180802 %G eng %R 10.1098/rsos.180802 %0 Journal Article %J J. Lightwave. Technol. %D 2018 %T Optofluidic Dye Lasers Based on Holey Fibers: Modeling and Performance Analysis %A Rashid, Zeeshan %A A. Jonáš %A Buczynski, Ryszard %A Alper Kiraz %K BF %K MF %B J. Lightwave. Technol. %V 36 %P 4114-4122 %G eng %R 10.1109/JLT.2018.2860684 %0 Journal Article %J Appl. Surf. Sci. %D 2018 %T Reversible switching of wetting properties and erasable patterning of polymer surfaces using plasma oxidation and thermal treatment %A Rashid, Zeeshan %A Atay, Ipek %A Soydan, Seren %A Yagci, M. Baris %A A. Jonáš %A Yilgor, Emel %A Alper Kiraz %A Yilgor, Iskender %K BF %K MF %B Appl. Surf. Sci. %V 441 %P 841-852 %G eng %R 10.1016/j.apsusc.2018.02.089 %0 Journal Article %J Phys. Rev. Lett. %D 2018 %T Robustness of Light-Transport Processes to Bending Deformations in Graded-Index Multimode Waveguides %A Flaes, D.E.B. %A Stopka, Jan %A S. Turtaev %A de Boer, J.F. %A Tyc, T. %A Tomáš Čižmár %K KF %K MF %B Phys. Rev. Lett. %V 120 %P 233901:1-5 %G eng %R 10.1103/PhysRevLett.120.233901 %0 Journal Article %J Sensors Actuators A %D 2018 %T Sensitivity of compositional measurement of high-pressure fluid mixtures using microcantilever frequency response %A Baloch, Shadi Khan %A A. Jonáš %A Alper Kiraz %A Alaca, B. Erdem %A Erkey, Can %K BF %K MF %B Sensors Actuators A %V 278 %P 111-126 %G eng %R /10.1016/j.sna.2018.05.025 %0 Journal Article %J Light: Sci. Appl. %D 2018 %T Subcellular spatial resolution achieved for deep-brain imaging in vivo using a minimally invasive multimode fiber %A Vasquez-Lopez, S.A. %A Turcotte, R. %A Koren, V. %A Ploschner, M. %A Padamsey, Z. %A Booth, M. %A Tomáš Čižmár %A Emptage, N.J. %K KF %K MF %B Light: Sci. Appl. %V 7 %P 110 %G eng %R 10.1038/s41377-018-0111-0 %0 Journal Article %J Nature Photon. %D 2018 %T Three-dimensional holographic optical manipulation through a high-numerical-aperture soft-glass multimode fibre %A I.T. Leite %A S. Turtaev %A Xin Jiang %A M Šiler %A Alfred Cuschieri %A Philip St. J. Russell %A Tomáš Čižmár %K KF %K MF %B Nature Photon. %V 12 %P 33–39 %G eng %R 10.1038/s41566-017-0053-8 %0 Journal Article %J Nature Commun. %D 2018 %T Transverse spin forces and non-equilibrium particle dynamics in a circularly polarized vacuum optical trap %A Vojtech Svak %A Oto Brzobohatý %A M Šiler %A P Jákl %A J. Kaňka %A P. Zemánek %A S. H. Simpson %K LF %K MF %B Nature Commun. %V 9 %P 5453 %G eng %R 10.1038/s41467-018-07866-8 %0 Journal Article %J ACS nano %D 2017 %T Accuracy and Mechanistic Details of Optical Printing of Single Au and Ag Nanoparticles %A Gargiulo, Juliàn %A Violi, Ianina L %A Cerrota, Santiago %A Lukáš Chvátal %A Cortès, Emiliano %A Perassi, Eduardo M %A Diaz, Fernando %A P. Zemánek %A Stefani, Fernando D %K LF %K MF %B ACS nano %V 11 %P 9678–9688 %G eng %R 10.1021/acsnano.7b04136 %0 Journal Article %J Future Microbiology %D 2017 %T Differentiation between Staphylococcus aureus and Staphylococcus epidermidis strains using Raman spectroscopy %A K. 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Zemánek %K BF %K MF %B Microscopy and Microanalysis %V 23 %P S1 %G eng %R 10.1017/S1431927617006456 %0 Journal Article %J Phys. Rev. Lett. %D 2017 %T Omnidirectional Transport in Fully Reconfigurable Two Dimensional Optical Ratchets %A Alejandro V. Arzola %A Villasante-Barahona, Mario %A Karen Volke-Sepúlveda %A P Jákl %A P. Zemánek %K LF %K MF %B Phys. Rev. Lett. %V 118 %P 138002 %G eng %R 10.1103/PhysRevLett.118.138002 %0 Journal Article %J Nano Lett. %D 2017 %T Optical Binding of Nanowires %A S. H. Simpson %A P. Zemánek %A Maragò, Onofrio M. %A Jones, Philip H. %A Hanna, Simon %K LF %K MF %B Nano Lett. %V 17 %P 3485-3492 %G eng %R 10.1021/acs.nanolett.7b00494 %0 Journal Article %J New Biotechnol. %D 2017 %T The presence of PHB granules in cytoplasm protects non-halophilic bacterial cells against the harmful impact of hypertonic environments %A S. Obruča %A P. Sedláček %A F. Mravec %A V. Krzyžánek %A J. Nebesářová %A O. Samek %A D. Kučera %A Pavla Benešová %A K. Hrubanová %A M. Milerová %A I. Márová %K BF %K MF %B New Biotechnol. %V 39 %P 10 %G eng %R 10.1016/j.nbt.2017.07.008 %0 Journal Article %J Sci. Rep. %D 2017 %T Rapid identification of staphylococci by Raman spectroscopy %A K. Rebrošová %A M Šiler %A O. Samek %A F. Růžička %A S. Bernatová %A V. Holá %A J Ježek %A P. Zemánek %A J. Sokolová %A P. Petráš %K BF %K MF %B Sci. Rep. %V 7 %P 14846 %G eng %R 10.1038/s41598-017-13940-w %0 Journal Article %J J. Opt. Soc. Am. B %D 2017 %T Thermal tuning of spectral emission from optically trapped liquid-crystal droplet resonators %A A. Jonáš %A Z. Pilát %A J Ježek %A Silva Bernatová %A T. Fořt %A P. Zemánek %A Mehdi Aas %A Alper Kiraz %K BF %K MF %B J. Opt. Soc. Am. B %V 34 %P 1855-1864 %G eng %R 10.1364/JOSAB.34.001855 %0 Journal Article %J Sci. Rep. %D 2017 %T Thermally induced micro-motion by inflection in optical potential %A M Šiler %A P Jákl %A Oto Brzobohatý %A Artem Ryabov %A Radim Filip %A P. Zemánek %K LF %K MF %B Sci. 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Express %V 24 %P 26382-26391 %G eng %R 10.1364/OE.24.026382 %0 Journal Article %J Opt. Lett. %D 2016 %T Direct measurement of the temperature profile close to an optically trapped absorbing particle %A M Šiler %A J Ježek %A P Jákl %A Z. Pilát %A P. Zemánek %K MF %B Opt. Lett. %V 41 %P 870-873 %G eng %R 10.1364/OL.41.000870 %0 Journal Article %J Nat. Phys. %D 2016 %T Direct measurements of the extraordinary optical momentum and transverse spin-dependent force using a nano-cantilever %A Antognozzi, M. %A Bermingham, C. R. %A Harniman, R. L. %A S. H. Simpson %A Senior, J. %A Hayward, R. %A Hoerber, H. %A Dennis, M. R. %A Bekshaev, A. Y. %A Bliokh, K. Y. %A Nori, F. %K MF %B Nat. Phys. %V 12 %P 731-735 %G eng %R 10.1038/nphys3732 %0 Journal Article %J Appl Microbiol Biotechnol %D 2016 %T Evaluation of 3-hydroxybutyrate as an enzyme-protective agent against heating and oxidative damage and its potential role in stress response of poly(3-hydroxybutyrate) accumulating cells %A S. 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Krzyžánek %K MF %B Microscopy and Microanalysis %V 22 %P S3 %G eng %R 10.1017/S1431927616006577 %0 Journal Article %J Journal of Optics %D 2016 %T Noise-to-signal transition of a Brownian particle in the cubic potential: I. general theory %A Radim Filip %A P. Zemánek %K MF %B Journal of Optics %V 18 %P 065401 %G eng %R 10.1088/2040-8978/18/6/065401 %0 Journal Article %J Journal of Optics %D 2016 %T Noise-to-signal transition of a Brownian particle in the cubic potential: II. optical trapping geometry %A P. Zemánek %A M Šiler %A Oto Brzobohatý %A P Jákl %A Radim Filip %K MF %B Journal of Optics %V 18 %P 065402 %G eng %R 10.1088/2040-8978/18/6/065401 %0 Journal Article %J Nano Lett. %D 2016 %T Photonic Torque Microscopy of the Nonconservative Force Field for Optically Trapped Silicon Nanowires %A Irrera, Alessia %A Magazzu, Alessandro %A Artoni, Pietro %A S. H. 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Sci. %D 2014 %T Candida parapsilosis Biofilm Identification by Raman Spectroscopy %A O. Samek %A K. Mlynariková %A Silva Bernatová %A J Ježek %A V. Krzyžánek %A M Šiler %A P. Zemánek %A F. Růžička %A V. Holá %A M. Mahelová %K MF %B Int. J. Mol. Sci. %V 15 %P 23924-23935 %G eng %R 10.3390/ijms151223924 %0 Journal Article %J Opt. Express %D 2014 %T Optical sorting of nonspherical and living microobjects in moving interference structures %A P Jákl %A Alejandro V. Arzola %A M Šiler %A Lukáš Chvátal %A Karen Volke-Sepúlveda %A P. Zemánek %K MF %B Opt. Express %V 22 %P 29746-29760 %G eng %R 10.1364/OE.22.029746 %0 Journal Article %J Opt. Express %D 2014 %T Rotation, oscillation and hydrodynamic synchronization of optically trapped oblate spheroidal microparticles %A Alejandro V. Arzola %A P Jákl %A Lukáš Chvátal %A P. Zemánek %K MF %B Opt. Express %V 22 %P 16207-16221 %G eng %R 10.1364/OE.22.016207 %0 Journal Article %J Phys. Rev. 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Express %V 20 %P 24304-24319 %G eng %R 10.1364/OE.20.024304 %0 Journal Article %J J. Appl. Phycol. %D 2012 %T Raman microspectroscopy of algal lipid bodies: beta-carotene quantification %A Z. Pilát %A Silva Bernatová %A J Ježek %A M. Šerý %A O. Samek %A P. Zemánek %A L. Nedbal %A M. Trtílek %K MF %B J. Appl. Phycol. %V 24 %P 541-546 %G eng %R 10.1007/s10811-011-9754-4 %0 Journal Article %J Appl. Phys. Lett. %D 2012 %T Speed enhancement of multi-particle chain in a traveling standing wave %A M Šiler %A Tomáš Čižmár %A P. Zemánek %K MF %B Appl. Phys. Lett. %V 100 %P 051103 %G eng %R 10.1063/1.3680234 %0 Journal Article %J Laser Phys. Lett. %D 2011 %T Characterization of oil-producing microalgae using Raman spectroscopy %A O. Samek %A P. Zemánek %A A. Jonáš %A Telle, H. H. %K MF %B Laser Phys. Lett. %V 8 %P 701–709 %G eng %R 10.1002/lapl.201110060 %0 Journal Article %J Appl. Phys. Lett. %D 2011 %T Dynamic size tuning of multidimensional optically bound matter %A Oto Brzobohatý %A Vítězslav Karásek %A Tomáš Čižmár %A P. Zemánek %K MF %B Appl. Phys. Lett. %V 99 %P 101105 %G eng %R 10.1063/1.3634007 %0 Journal Article %J Laser Phys. Lett. %D 2011 %T The holographic optical micro-manipulation system based on counter-propagating beams %A Tomáš Čižmár %A Oto Brzobohatý %A Kishan Dholakia %A P. Zemánek %K MF %B Laser Phys. Lett. %V 8 %P 50–56 %G eng %R 10.1002/lapl.201010100 %0 Journal Article %J J. Opt. %D 2011 %T Parametric study of optical forces acting upon nanoparticles in a single, or a standing, evanescent wave %A M Šiler %A P. Zemánek %K MF %B J. Opt. %V 13 %P 044016:1–9 %G eng %R 10.1088/2040-8978/13/4/044016 %0 Journal Article %J Opt. Express %D 2011 %T Static and dynamic behavior of two optically bound microparticles in a standing wave %A Oto Brzobohatý %A Vítězslav Karásek %A M Šiler %A J. Trojek %A P. Zemánek %K MF %B Opt. Express %V 19 %P 19613–19626 %G eng %R 10.1364/OE.19.019613 %0 Journal Article %J Langmuir %D 2010 %T Diffusive Mixing of Polymers Investigated by Raman Microspectroscopy and Microrheology %A A. Jonáš %A De Luca, A. C. %A Pesce, G. %A Rusciano, G. %A A. Sasso %A Caserta, S. %A Guido, S. %A Marrucci, G. %K MF %B Langmuir %V 26 %P 14223-14230 %G eng %R 10.1021/la101498h %0 Journal Article %J Opt. Express %D 2010 %T Experimental and theoretical determination of optical binding forces %A Oto Brzobohatý %A Tomáš Čižmár %A Vítězslav Karásek %A M Šiler %A Kishan Dholakia %A P. Zemánek %K MF %B Opt. Express %V 18 %P 25389–25402 %G eng %R 10.1364/OE.18.025389 %0 Journal Article %J Rev. Mod. Phys. %D 2010 %T Gripped by light: Optical binding %A Kishan Dholakia %A P. Zemánek %K MF %B Rev. Mod. Phys. %V 82 %P 1767–1791 %G eng %R 10.1103/RevModPhys.82.1767 %0 Journal Article %J New. J. Phys. %D 2010 %T Particle jumps between optical traps in a one-dimensional optical lattice %A M Šiler %A P. Zemánek %K MF %B New. J. Phys. %V 12 %P 083001:1–20 %G eng %R 10.1088/1367-2630/12/8/083001 %0 Journal Article %J Laser Phys. Lett. %D 2010 %T The potential of Raman spectroscopy for the identification of biofilm formation by Staphylococcus epidermidis %A O. Samek %A Al-Marashi, J. F. M. %A Telle, H. H. %K MF %B Laser Phys. Lett. %V 7 %P 378–383 %G eng %9 Article %R 10.1002/lapl.200910154 %0 Journal Article %J Sensors %D 2010 %T Raman Microspectroscopy of Individual Algal Cells: Sensing Unsaturation of Storage Lipids in vivo %A O. Samek %A A. Jonáš %A Z. Pilát %A P. Zemánek %A L. Nedbal %A Tříska, J. %A Kotas, P. %A M. Trtílek %K MF %B Sensors %V 10 %P 8635–8651 %G eng %R 10.3390/s100908635 %0 Journal Article %J Chem. Phys. Chem. %D 2009 %T Detecting Sequential Bond Formation Using Three-Dimensional Thermal Fluctuation Analysis %A Bartsch, Tobias F. %A Fisinger, Samo %A Kochanczyk, Martin D. %A Huang, Rongxin %A A. Jonáš %A Florin, Ernst-Ludwig %K MF %B Chem. Phys. Chem. %V 10 %P 1541-1547 %G eng %R 10.1002/cphc.200900211 %0 Journal Article %J Phys. Rev. Lett. %D 2009 %T Direct Measurement of the Nonconservative Force Field Generated by Optical Tweezers %A Wu, Pinyu %A Huang, Rongxin %A Tischer, Christian %A A. Jonáš %A Florin, Ernst-Ludwig %K MF %B Phys. Rev. Lett. %V 103 %P 108101 %G eng %R 10.1103/PhysRevLett.103.108101 %0 Journal Article %J Opt. Express %D 2009 %T Extreme axial optical force in a standing wave achieved by optimized object shape %A J. Trojek %A Vítězslav Karásek %A P. Zemánek %K MF %B Opt. Express %I OSA %V 17 %P 10472–10488 %G eng %R 10.1364/OE.17.010472 %0 Journal Article %J J. Opt. A: Pure Appl. Opt. %D 2009 %T Longitudinal optical binding of several spherical particles studied by the coupled dipole method %A Vítězslav Karásek %A Oto Brzobohatý %A P. Zemánek %K MF %B J. Opt. A: Pure Appl. Opt. %V 11 %P 034009 %G eng %R 10.1088/1464-4258/11/3/034009 %0 Journal Article %J Opt. Express %D 2008 %T High quality quasi-Bessel beam generated by round-tip axicon %A Oto Brzobohatý %A Tomáš Čižmár %A P. Zemánek %K MF %B Opt. Express %V 16 %P 12688–12700 %G eng %R 10.1364/OE.16.012688 %0 Journal Article %J Electophoresis %D 2008 %T Light at work: The use of optical forces for particle manipulation, sorting, and analysis. %A A. Jonáš %A P. Zemánek %K MF %B Electophoresis %V 29 %P 4813–4851 %G eng %R 10.1002/elps.200800484 %0 Journal Article %J Phys. Rev. Lett. %D 2008 %T Long-range one-dimensional longitudinal optical binding %A Vítězslav Karásek %A Tomáš Čižmár %A Oto Brzobohatý %A P. Zemánek %A V. Garcés-Chávez %A Kishan Dholakia %K MF %B Phys. Rev. Lett. %V 101 %P 143601 %G eng %R 10.1103/PhysRevLett.101.143601 %0 Journal Article %J Appl. Phys. Lett. %D 2008 %T Static optical sorting in a laser interference field %A P Jákl %A Tomáš Čižmár %A M. Šerý %A P. Zemánek %K MF %B Appl. Phys. Lett. %V 92 %P 161110:1–3 %G eng %R 10.1063/1.2913759 %0 Journal Article %J New. J. Phys. %D 2008 %T Surface delivery of a single nanoparticle under moving evanescent standing-wave illumination %A M Šiler %A Tomáš Čižmár %A A. Jonáš %A P. Zemánek %K MF %B New. J. Phys. %V 10 %P 113010 %G eng %R 10.1088/1367-2630/10/11/113010 %0 Journal Article %J J. Opt. A: Pure Appl. Opt. %D 2007 %T Analytical description of longitudinal optical binding of two spherical nanoparticles %A Vítězslav Karásek %A P. Zemánek %K MF %B J. Opt. A: Pure Appl. Opt. %V 9 %P S215–S220 %G eng %R 10.1088/1464-4258/9/8/S14 %0 Journal Article %J J. Opt. A: Pure Appl. Opt. %D 2007 %T Axial optical trap stiffness influenced by retro-reflected beam %A P Jákl %A M. Šerý %A J Ježek %A M. Liška %A P. Zemánek %K MF %B J. Opt. A: Pure Appl. Opt. %V 9 %P S251–S255 %G eng %R 10.1088/1464-4258/9/8/S19 %0 Journal Article %J Methods in Cell Biology %D 2007 %T Cellular and colloidal separation using optical forces %A Kishan Dholakia %A MacDonald, M. P. %A P. Zemánek %A Tomáš Čižmár %K MF %B Methods in Cell Biology %V 82 %P 467–495 %G eng %R 10.1016/S0091-679X(06)82017-0 %0 Journal Article %J Opt. Commun. %D 2007 %T Optical forces acting on a nanoparticle placed into an interference evanescent field %A M Šiler %A P. Zemánek %K MF %B Opt. Commun. %V 275 %P 409–420 %G eng %R 10.1016/j.optcom.2007.03.074 %0 Journal Article %J Opt. Express %D 2007 %T Optical tracking of spherical micro-objects in spatially periodic interference fields %A Tomáš Čižmár %A P. Zemánek %K MF %B Opt. Express %V 15 %P 2262–2272 %G eng %R 10.1364/OE.15.002262 %0 Journal Article %J J. Optoel Adv. Mater. %D 2007 %T Opto-fluidic micromanipulation system based on integrated polymer waveguides %A P Jákl %A M. Šerý %A J Ježek %A P. Zemánek %A Ormos, P. %A Valkai, S. %A Kelemen, L. %K MF %B J. Optoel Adv. Mater. %V 9 %P 2148-2151 %G eng %0 Journal Article %J Opt. Express %D 2007 %T Transverse particle dynamics in a Bessel beam %A Milne, Graham %A Kishan Dholakia %A McGloin, David %A Karen Volke-Sepúlveda %A P. Zemánek %K MF %B Opt. Express %I OSA %V 15 %P 13972–13987 %G eng %U http://www.opticsexpress.org/abstract.cfm?URI=oe-15-21-13972 %R 10.1364/OE.15.013972 %0 Journal Article %J Appl. Phys. B %D 2006 %T Analysis of optical binding in one dimension %A Vítězslav Karásek %A Kishan Dholakia %A P. Zemánek %K MF %B Appl. Phys. B %V 84 %P 149–156 %G eng %R 10.1007/s00340-006-2297-8 %0 Journal Article %J Opt. Express %D 2006 %T Formation of long and thin polymer fiber using nondiffracting beam %A J Ježek %A Tomáš Čižmár %A V. Neděla %A P. Zemánek %K MF %B Opt. Express %V 14 %P 8506-8515 %G eng %R 10.1364/OE.14.008506 %0 Journal Article %J Appl. Phys. B %D 2006 %T Optical forces generated by evanescent standing waves and their usage for sub-micron particle delivery %A M Šiler %A Tomáš Čižmár %A M. Šerý %A P. Zemánek %K MF %B Appl. Phys. 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