@article {4129, title = {Assembly for semi-correlation analysis of samples using cryogenic scanning electron microscopy and cryogenic Raman micro-spectroscopy}, journal = {MEASUREMENT SCIENCE AND TECHNOLOGY}, volume = {36}, year = {2025}, month = {MAY 31}, pages = {055903}, keywords = {BF, MF}, issn = {0957-0233}, doi = {10.1088/1361-6501/adc94a}, author = {Laznicka, Tomas and Kizovsk{\'y}, Martin and Hrubanov{\'a}, Kamila and Je{\v z}ek, Jan and Mrazova, Katerina and Obru{\v c}a, Stanislav and Samek, Ota and Krzy{\v z}{\'a}nek, Vladislav} } @inbook {4132, title = {Chapter 26 - Hyphenated Raman and laser spectroscopy for the characterization of microplastics in tissues}, booktitle = {Applied Raman Spectroscopy}, year = {2025}, pages = {441-451}, publisher = {Elsevier}, organization = {Elsevier}, abstract = {

This chapter is dedicated to the possibility of combining Raman spectroscopy with other spectroscopic methods, namely laser-induced breakdown spectroscopy (LIBS) in the detection and characterization of microplastics embedded in tissues of selected model organisms. The idea is to take advantage of the complementarity of the two methods, which originates in the way of laser-tissue interaction that both techniques utilize for sample analysis. Their joint use yields complete chemical information, that is, Raman spectroscopy provides molecular information, whereas LIBS provides atomic information as is well-described in the literature. Ultimately, the tandem LIBS{\textendash}Raman analysis can be done from the same spot of the sample. Moreover, these two methods need very similar components and thus can share the majority of the laboratory setup. The chapter gives an overview of hyphenated Raman and LIBS systems, advancements in this field, and options for data processing of joint Raman and LIBS analyses. Data fusion of Raman spectroscopy and LIBS is also discussed. Special attention will be given to the detection and characterization of microplastics using Raman and LIBS systems, as microplastic pollution has attracted considerable attention in recent years, with news of microplastic detection in recent areas and also in human bodies resonating publicly. Raman spectroscopy may be utilized in the detection of microplastics and recent works support this. With the help of LIBS, which can elucidate further the potential risks of weathered microplastics, the hyphenated approach may be the way forward for in situ detection and characterization of microplastics.

}, keywords = {BF, MF}, isbn = {978-0-443-21834-7}, doi = {https://doi.org/10.1016/B978-0-443-21834-7.00026-8}, url = {https://www.sciencedirect.com/science/article/pii/B9780443218347000268}, author = {Pavel Po{\v r}{\'\i}zka and Daniel Holub and Martin Kizovsk{\'y} and Ota Samek and Jozef Kaiser and Gabriela Kal{\v c}{\'\i}kov{\'a}}, editor = {Vivek Kumar Singh} } @article {4125, title = {Compact vacuum setup for laser induced plasma etching with optical emission spectrum monitoring}, journal = {Journal of Vacuum Science \& Technology B}, volume = {43}, year = {2025}, month = {04}, pages = {034202}, abstract = {

Reactive ion etching and reactive ion beam etching are widely used processes in the semiconductor industry but face challenges due to their high cost, energy demands, and maintenance complexity. Femtosecond laser micromachining has emerged as a versatile and precise method for microfabrication, but it often results in suboptimal surface quality, which requires postprocessing. Laser-induced plasma etching (LIPE) presents a promising solution, achieving low surface roughness and efficient material removal rates. Here, we investigate the LIPE process by utilizing a femtosecond laser setup with optimized optical components and a custom-designed compact vacuum chamber, enabling precise control and monitoring of the reactive gas environment for plasma generation and etching. The effects of numerical aperture, working distance, and laser energy thresholds on plasma ignition and plume formation were examined. Preliminary results demonstrate plasma ignition in air and SF6 gas with laser pulse energy thresholds between 15 and 20 μJ using a 10{\texttimes} magnification microscope objective. The spectral analysis of the plasma generated in the SF6 gas provides insights into plasma dynamics and enables real-time process monitoring. This work establishes foundational parameters for optimizing LIPE setups and advancing precision etching applications.

}, keywords = {AIF, MF}, issn = {2166-2746}, doi = {10.1116/6.0004296}, url = {https://doi.org/10.1116/6.0004296}, author = {Silhan, Lukas and Arregi, Jon Ander and Plichta, Tom{\'a}{\v s} and Vaculik, Ondrej and Novotny, Jan and {\v S}er{\'y}, Mojm{\'\i}r} } @article {4087, title = {Dynamic formation of arrays of interacting optical spatial solitons under light-sheet illumination}, journal = {Optics Letters}, volume = {50}, year = {2025}, month = {Jul}, pages = {4318{\textendash}4321}, keywords = {LF, MF}, doi = {10.1364/OL.561703}, url = {https://opg.optica.org/ol/abstract.cfm?URI=ol-50-13-4318}, author = {Brzobohat{\'y}, O. and Chv{\'a}tal, L. and Jon{\'a}{\v s}, A. and Zem{\'a}nek, P.} } @article {4128, title = {Impact of Collagen on the Rheological and Transport Properties of Agarose Hydrogels}, journal = {Gels}, volume = {11}, year = {2025}, pages = {396}, abstract = {

This work investigated how collagen addition affects the rheological and transport properties of agarose hydrogels. Collagen did not affect the rheological character of hydrogels (i.e., the overall shape of amplitude and frequency response curves) but changed their viscoelastic moduli and mesh size dependent on the concentration of both constituents. The diffusion coefficients of the oppositely charged model dyes eosin B and methylene blue were determined in all hydrogels and demonstrated a profound effect of electrostatic interactions. Comparison with similar work with fibroin addition showed that while the effects of these proteins on the viscoelastic properties of a polysaccharide network can be similar, their impact on network transport properties may be different.

}, keywords = {AIF, MF}, issn = {2310-2861}, doi = {10.3390/gels11060396}, url = {https://www.mdpi.com/2310-2861/11/6/396}, author = {Richterov{\'a}, Veronika and Gjevik, Al{\v z}b{\v e}ta and Vaculik, Ondrej and Vejrosta, Jakub and Peka{\v r}, Miloslav} } @article {4124, title = {Nanomechanical state amplifier based on optical inverted pendulum}, journal = {Communications Physics}, volume = {8}, year = {2025}, pages = {276}, keywords = {LF, MF}, issn = {2399-3650}, doi = {10.1038/s42005-025-02193-z}, url = {https://www.nature.com/articles/s42005-025-02193-z}, author = {Ducha{\v n}, Martin and {\v S}iler, Martin and J{\'a}kl, Petr and Brzobohat{\'y}, Oto and Rakhubovsky, Andrey and Filip, Radim and Zem{\'a}nek, Pavel} } @conference {4126, title = {Preparation and pilot experiments on microfluidic chip with surface acoustic waves}, booktitle = {23rd Slovak-Czech-Polish Optical Conference on Wave and Quantum Aspects of Contemporary Optics}, year = {2025}, publisher = {International Society for Optics and Photonics}, organization = {International Society for Optics and Photonics}, keywords = {AIF, MF}, doi = {10.1117/12.3056740}, url = {https://doi.org/10.1117/12.3056740}, author = {J. Vejrosta and S. Cabalov{\'a} and T. Plichta and M. {\v S}er{\'y} and T. Ma{\v n}ka and O. Samek and P. Zem{\'a}nek}, editor = {Du{\v s}an Pudi{\v s} and Daniel Jandura and Ivana Lettrichov{\'a}} } @article {4131, title = {Stability of masking materials for pattern transfer of lithographic masks into fused silica by atmospheric pressure plasma jet etching}, journal = {Micro and Nano Engineering}, volume = {28}, year = {2025}, pages = {100309}, abstract = {

Masking of thin films and bulk materials is traditionally applied for the transfer of micron patterns into the functional material according to the requirements of the application. For optical purposes, lithographically produced micron patterns are transferred by plasma/ion etching, which is a traditional technology in microelectronics and other micron technologies. However, pattern transfer by atmospheric pressure plasma etching can help to save time and cost for a future sustainable production. Therefore, the pattern transfer of lithographic resist masks into fused silica using atmospheric pressure reactive plasma jets (APPJ) was studied as a new approach of micropatterning. First the etch rates of the potential masking materials, e.g. photoresists, as well as of fused silica as substrate are studied in dependence on the APPJ etching parameters, in particular on the gas composition (O2/CF4) and the dwell time of the APPJ tool{\textquoteright}s footprint. Typical etch rates of the masking materials are in the range of 140 to 370\ nm{\textperiodcentered}s-1 whereas the fused silica has a rate of 25 to 80\ nm{\textperiodcentered}s-1. The surface morphology of masking materials changes during etching and features additional nanoscale roughness and waviness. The surface roughness of the etched masking materials and the fused silica are 2 to 5\ nm rms and 1.5\ nm rms for etch depths of \~{}3000\ nm and\ \~{}\ 600\ nm, respectively. Finally, the pattern transfer by APPJ of a diffraction grating with a period of 15\ μm, depth of 230\ nm and a roughness below 2\ nm rms into fused silica was demonstrated.

}, keywords = {AIF, MF}, issn = {2590-0072}, doi = {https://doi.org/10.1016/j.mne.2025.100309}, url = {https://www.sciencedirect.com/science/article/pii/S2590007225000152}, author = {Robert Heinke and Luk{\'a}{\v s} {\v S}ilhan and Martin Ehrhardt and Pierre Lorenz and Joachim Zajadacz and Jens Bauer and Thomas Arnold and Mojm{\'\i}r {\v S}er{\'y} and Klaus Zimmer} } @article {4130, title = {Surface-Enhanced Raman Spectroscopy for Adenine Detection in Five Selected Bacterial Strains Under Stress Conditions}, journal = {SENSORS}, volume = {25}, year = {2025}, month = {JUL 26}, pages = {4629}, keywords = {BF, MF}, doi = {10.3390/s25154629}, author = {Ghazalova, Mona and Modlitbova, Pavlina and Samek, Ota and Rebro{\v s}ov{\'a}, Katar{\'\i}na and {\v S}iler, Martin and Je{\v z}ek, Jan and Pil{\'a}t, Zden{\v e}k} } @article {3864, title = {Biomedical Optics Express Feature Issue Introduction: Optical Manipulation and Its Applications (OMA) 2023}, journal = {BIOMEDICAL OPTICS EXPRESS}, volume = {15}, year = {2024}, month = {FEB 1}, pages = {1192-1194}, keywords = {BF, MF}, issn = {2156-7085}, doi = {10.1364/BOE.519305}, author = {Jones, Philip and Bernatov{\'a}, Silvie and Kotsifaki, Domna G.} } @conference {3997, title = {Design of Setup for Laser Induced Plasma Etching}, booktitle = {2024 37th International Vacuum Nanoelectronics Conference (IVNC)}, year = {2024}, keywords = {AIF, MF}, doi = {10.1109/IVNC63480.2024.10652276}, author = {Silhan, Lukas and Novotny, Jan and Plichta, Tom{\'a}{\v s} and Je{\v z}ek, Jan and Vaculik, Ondrej and {\v S}er{\'y}, Mojm{\'\i}r} } @article {3995, title = {Exploiting Complex Media Photonics to Illuminate Brain{\textquoteright}s Hidden Depth}, journal = {NEUROPHOTONICS}, volume = {11}, year = {2024}, month = {SEP 1}, pages = {S11501}, keywords = {KF, MF}, issn = {2329-423X}, doi = {10.1117/1.NPh.11.S1.S11501}, author = {Uhlirova, Hana and Cizmar, Tomas and Pakan, Janelle M. P. and Gomes, Andre} } @inbook {3938, title = {Functional Interlayers Developed to Control Interfacial Adhesion in Polymer Composites Reinforced with Glass and Basalt Fibers}, booktitle = {Progress in Adhesion and Adhesives}, year = {2024}, pages = {119{\textendash}188}, publisher = {Wiley}, organization = {Wiley}, edition = {Vol. 8}, chapter = {3}, keywords = {AIF, MF}, isbn = {9781394238200}, doi = {10.1002/9781394238231.ch3}, author = {Plichta, Tom{\'a}{\v s} and {\v C}ech, Vladim{\'\i}r}, editor = {Mittal, K. L.} } @article {4046, title = {Generating Airy beams through multimode fibres}, journal = {Optics Express}, volume = {32}, year = {2024}, note = {

Publisher: Optica Publishing Group

}, pages = {6838{\textendash}6847}, abstract = {

Focussing light through a multimode fibre (MMF) is the basis of holographic endoscopes, which currently enable detailed imaging of deep tissue. Achieving high fidelity and purity diffraction-limited foci has been shown to be possible, when fully controlling the amplitude, phase, and two orthogonal polarisation states of the input field. Yet, generating more complex field distributions with similar performance remains to be assessed. Here, we demonstrate the generation of Airy beams through an MMF containing in excess of 90 \% of the optical power delivered by the fibre. We discuss two distinct methods for generating optical landscapes: the direct field and the Fourier domain synthesis. Moreover, we showcase the flexibility of the Fourier domain synthesis to modify the generated beam.

}, keywords = {KF, MF}, issn = {1094-4087}, doi = {10.1364/OE.506926}, url = {https://opg.optica.org/oe/abstract.cfm?uri=oe-32-5-6838}, author = {Mich{\'a}lkov{\'a}, Ivana and Colombel, Simon and Gomes, Andr{\'e} D. and Cizmar, Tomas} } @article {3991, title = {MicrobioRaman: an open-access web repository for microbiological Raman spectroscopy data}, journal = {NATURE MICROBIOLOGY}, volume = {9}, year = {2024}, month = {MAY}, keywords = {BF, MF}, issn = {2058-5276}, doi = {10.1038/s41564-024-01656-3}, author = {Lee, Kang Soo and Landry, Zachary and Athar, Awais and Alcolombri, Uria and Ayutthaya, Pratchaya Pramoj Na and Berry, David and de Bettignies, Philippe and Cheng, Ji-Xin and Csucs, Gabor and Cui, Li and Deckert, Volker and Dieing, Thomas and Dionne, Jennifer and Doskocil, Ondrej and D{\textquoteright}Souza, Glen and Garcia-Timermans, Cristina and Gierlinger, Notburga and Goda, Keisuke and Hatzenpichler, Roland and Henshaw, Richard J. and Huang, Wei E. and Iermak, Ievgeniia and Ivleva, Natalia P. and Kneipp, Janina and Kubryk, Patrick and Kuesel, Kirsten and Lee, Tae Kwon and Lee, Sung Sik and Ma, Bo and Martinez-Perez, Clara and Matousek, Pavel and Meckenstock, Rainer U. and Min, Wei and Mojzes, Peter and Mueller, Oliver and Kumar, Naresh and Nielsen, Per Halkjaer and Notingher, Ioan and Palatinszky, Marton and Pereira, Fatima C. and Pezzotti, Giuseppe and Pil{\'a}t, Zden{\v e}k and Plesinger, Filip and Popp, Juergen and Probst, Alexander J. and Riva, Alessandra and Saleh, Amr. A. E. and Samek, Ota and Sapers, Haley M. and Schubert, Olga T. and Stubbusch, Astrid K. M. and Tadesse, Loza F. and Taylor, Gordon T. and Wagner, Michael and Wang, Jing and Yin, Huabing and Yue, Yang and Zenobi, Renato and Zini, Jacopo and Sarkans, Ugis and Stocker, Roman} } @article {3992, title = {Microplastics in animal nutrition: Occurrence, spread, and hazard in animals}, journal = {JOURNAL OF AGRICULTURE AND FOOD RESEARCH}, volume = {17}, year = {2024}, month = {SEP}, pages = {101258}, keywords = {BF, MF}, issn = {2666-1543}, doi = {10.1016/j.jafr.2024.101258}, author = {Khan, Aamir and Qadeer, Abdul and Wajid, Abdul and Ullah, Qudrat and Rahman, Sajid Ur and Ullah, Kaleem and Safi, Sher Zaman and Ticha, Lenka and Skalickova, Sylvie and Chilala, Pompido and Bernatov{\'a}, Silvie and Samek, Ota and Horky, Pavel} } @article {3907, title = {PT-like phase transition and limit cycle oscillations in non-reciprocally coupled optomechanical oscillators levitated in vacuum}, journal = {Nat. Phys.}, year = {2024}, note = {

Publisher: Nature Publishing Group

}, pages = {1{\textendash}7}, abstract = {

Nanoparticles levitated in an optical trap provide a versatile platform to study mechanical oscillators in a controlled environment with tuneable parameters. Recently, it has become possible to couple two of these optomechanical oscillators. Here we demonstrate the collective non-Hermitian dynamics of such a pair of non-conservatively coupled oscillators. We take advantage of the tunability of the optical interactions between the particles in our system and set the optical interaction between the particles to be purely non-reciprocal. By continuously varying the relative power of the trapping beams, we take the system through a transition similar to a parity{\textendash}time phase transition. A Hopf bifurcation at a critical point results in the formation of collective limit cycle oscillations, resembling those observed in phonon lasers. These coupled levitated oscillators provide a platform for exceptional point optomechanical sensing and can be extended to multi-particle systems, paving the way for the development of topological optomechanical media.

}, keywords = {LF, MF}, issn = {1745-2481}, doi = {10.1038/s41567-024-02590-1}, url = {https://www.nature.com/articles/s41567-024-02590-1}, author = {Li{\v s}ka, Vojt{\v e}ch and Zem{\'a}nkov{\'a}, Tereza and J{\'a}kl, Petr and {\v S}iler, Martin and Simpson, Stephen H. and Zem{\'a}nek, Pavel and Brzobohat{\'y}, Oto} } @article {3989, title = {Raman microspectroscopy and laser-induced breakdown spectroscopy for the analysis of polyethylene microplastics in human soft tissues}, journal = {Heliyon}, volume = {10}, year = {2024}, pages = {e37844}, abstract = {

People are exposed to microplastics (MPs) on a large scale in everyday life. However, it is not clear whether MPs can also be distributed and retained in certain tissues. Therefore, the development of analytical methods capable of detecting MPs in specific human organs/tissues is of utmost importance. In this study, the use and combination of spectroscopic techniques, namely Raman microspectroscopy and laser-induced breakdown spectroscopy (LIBS), was tested for the detection of polyethylene (PE) MPs in human tonsils. Preliminary results showed that Raman microspectroscopy was able to detect MPs down to 1\ μm in size and LIBS down to 10\ μm. In the next step, human tonsils were spiked with PE MPs, and digested. The filtered particles were analyzed using Raman microspectroscopy and LIBS, and complemented by X-ray fluorescence (XRF). The results showed that Raman microspectroscopy could reliably detect PE MPs in spiked human tonsils, while LIBS and XRF served as a reference analytical method to characterize particles that could not be classified by Raman microspectroscopy for their non-organic origin. The results of this study, supported by a current feasibility study conducted on clinical samples, demonstrated the reliability and feasibility of this approach for monitoring MPs in biotic samples.

}, keywords = {BF, MF}, issn = {2405-8440}, doi = {https://doi.org/10.1016/j.heliyon.2024.e37844}, url = {https://www.sciencedirect.com/science/article/pii/S2405844024138753}, author = {Vikt{\'o}ria Parobkov{\'a} and Daniel Holub and Martin Kizovsk{\'y} and Gabriela Kal{\v c}{\'\i}kov{\'a} and Ula Rozman and Milan Ur{\'\i}k and Karel Novotn{\'y} and Ota Samek and Tom{\'a}{\v s} Zikmund and Pavel Po{\v r}{\'\i}zka and Jozef Kaiser} } @article {3856, title = {Simulation of optomechanical interaction of levitated nanoparticle with photonic crystal micro cavity}, journal = {Opt. Express}, volume = {32}, year = {2024}, month = {Feb}, pages = {7185{\textendash}7196}, abstract = {

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 {\texttimes} 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.

}, keywords = {LF, MF}, doi = {10.1364/OE.515202}, url = {https://opg.optica.org/oe/abstract.cfm?URI=oe-32-5-7185}, author = {Tade{\'a}{\v s} Ma{\v n}ka and Martin {\v S}iler and Vojt{\v e}ch Li{\v s}ka and Pavel Zem{\'a}nek and Mojm{\'\i}r {\v S}er{\'y} and Oto Brzobohat{\'y}} } @article {3994, title = {{\textquoteleft}{\textquoteleft}There{\textquoteright}s plenty of room at the bottom{\textquoteright}{\textquoteright}: deep brain imaging with holographic endo-microscopy}, journal = {NEUROPHOTONICS}, volume = {11}, year = {2024}, month = {SEP 1}, keywords = {KF, MF}, issn = {2329-423X}, doi = {10.1117/1.NPh.11.S1.S11504}, author = {Uhlirova, Hana and Stib{\r u}rek, Miroslav and Pik{\'a}lek, Tom{\'a}{\v s} and Gomes, Andre and Turtaev, Sergey and Kolbabkova, Petra and Cizmar, Tomas} } @article {3865, title = {Unraveling the ecotoxicological effects of micro and nano-plastics on aquatic organisms and human health}, journal = {Frontiers in Environmental Science}, volume = {12}, year = {2024}, abstract = {

Plastic pollution ranks among the most severe environmental disasters caused by humans, generating millions of tonnes of waste annually. The extensive and unregulated use of plastics has led to ecotoxicity and environmental imbalance. Microplastics (MPs) are prevalent in aquatic environments, and these MPs further degrade into even smaller particles known as nano-plastics (NPs). Both MPs and NPs impact the environment by readily absorbing organic pollutants and pathogens from their surroundings, owing to their bigger surface area to volume ratio. This review focuses on the source of origin, bioaccumulation, and potential impact of MPs and NPs on aquatic organisms and human health. Additionally, the review explores various methods employed for identification and quantification of these particles in aquatic ecosystems. Sufficient information is available on their characteristics, distributions, and effects on marine ecosystems compared with freshwater ecosystems. For plastic particles \<10\ μm, more toxicological effects were observed compared with larger size particles, in aquatic life. Understanding the mechanism of action and ecotoxicological effects of micro/nano-plastics on the health of aquatic life across various trophic levels, as well as human health, is of utmost importance. We address knowledge gaps and provide insights into future research approaches for a better understanding of the interactive mechanisms between binary pollutants.

}, keywords = {BF, MF}, issn = {2296-665X}, doi = {10.3389/fenvs.2024.1390510}, url = {https://www.frontiersin.org/articles/10.3389/fenvs.2024.1390510}, author = {Naz, Saima and Chatha, Ahmad Manan Mustafa and Khan, Nisar Ahmed and Ullah, Qudrat and Zaman, Faisal and Qadeer, Abdul and Khan, Ibrar Muhammad and Danabas, Durali and Kiran, Azka and Skalickova, Sylvie and Bernatov{\'a}, Silvie and Khan, Muhammad Zahoor and Horky, Pavel} } @article {3727, title = {110 mu m thin endo-microscope for deep-brain in vivo observations of neuronal connectivity, activity and blood flow dynamics}, journal = {NATURE COMMUNICATIONS}, volume = {14}, year = {2023}, month = {APR 5}, pages = {1897}, keywords = {KF, MF}, doi = {10.1038/s41467-023-36889-z}, author = {Stib{\r u}rek, Miroslav and Ondr{\'a}{\v c}kov{\'a}, Petra and Tuckova, Tereza and Turtaev, Sergey and {\v S}iler, Martin and Pik{\'a}lek, Tom{\'a}{\v s} and J{\'a}kl, Petr and Gomes, Andre and Krejci, Jana and Kolbabkova, Petra and Uhlirova, Hana and Cizmar, Tomas} } @article {3804, title = {Analysis of the machinability of different types of sintered carbides with WEDM in both water and oil baths}, journal = {The International Journal of Advanced Manufacturing Technology}, year = {2023}, abstract = {

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 {\textmu}m, was recorded for the WKP23S sample when machined in oil and Ra 0.9 {\textmu}m when the same material was machined in water.

}, keywords = {AIF, MF}, issn = {1433-3015}, doi = {10.1007/s00170-023-10913-4}, url = {https://doi.org/10.1007/s00170-023-10913-4}, author = {Mouralova, Katerina and Benes, Libor and Prokes, Tomas and Zahradnicek, Radim and Fries, Jiri and Plichta, Tom{\'a}{\v s}} } @inbook {3798, title = {Application of Aerogels in Optical Devices}, booktitle = {Springer Handbook of Aerogels}, year = {2023}, pages = {1431{\textendash}1454}, publisher = {Springer International Publishing}, organization = {Springer International Publishing}, address = {Cham}, keywords = {LF, MF}, isbn = {978-3-030-27322-4}, doi = {10.1007/978-3-030-27322-4_56}, url = {https://doi.org/10.1007/978-3-030-27322-4_56}, author = {Ozbakir, Yaprak and Jonas, Alexandr and Kiraz, Alper and Erkey, Can}, editor = {Aegerter, Michel A. and Leventis, Nicholas and Koebel, Matthias and Steiner III, Stephen A.} } @article {3737, title = {Aspergillus niger as a cell factory for the production of pyomelanin, a molecule with UV-C radiation shielding activity}, journal = {Frontiers in Microbiology}, volume = {14}, year = {2023}, keywords = {BF, MF}, issn = {1664-302X}, doi = {10.3389/fmicb.2023.1233740}, url = {https://www.frontiersin.org/articles/10.3389/fmicb.2023.1233740}, author = {Koch, Stella Marie and Freidank-Pohl, Carsten and Siontas, Oliver and Cortesao, Marta and Mota, Afonso and Runzheimer, Katharina and Jung, Sascha and Rebro{\v s}ov{\'a}, Katar{\'\i}na and {\v S}iler, Martin and Moeller, Ralf and Meyer, Vera} } @article {3726, title = {Bayesian Estimation of Experimental Parameters in Stochastic Inertial Systems: Theory, Simulations, and Experiments with Objects Levitated in Vacuum}, journal = {Phys. Rev. Appl.}, volume = {19}, year = {2023}, month = {Jun}, pages = {064059}, keywords = {LF, MF}, doi = {10.1103/PhysRevApplied.19.064059}, url = {https://link.aps.org/doi/10.1103/PhysRevApplied.19.064059}, author = {{\v S}iler, M. and Svak, V. and Jon{\'a}{\v s}, A. and Simpson, S.H. and Brzobohat{\'y}, O. and Zem{\'a}nek, P.} } @article {3753, title = {Cold damping of levitated optically coupled nanoparticles}, journal = {Optica}, volume = {10}, year = {2023}, pages = {1203{\textendash}1209}, keywords = {LF, MF}, doi = {10.1364/OPTICA.496072}, url = {https://opg.optica.org/optica/abstract.cfm?URI=optica-10-9-1203}, author = {Vojt{\v e}ch Li{\v s}ka and Tereza Zem{\'a}nkov{\'a} and Vojtech Svak and Petr J{\'a}kl and Jan Je{\v z}ek and Martin Br{\'a}neck{\'y} and Stephen H. Simpson and Pavel Zem{\'a}nek and Oto Brzobohat{\'y}} } @article {3807, title = {Controlling light propagation in multimode fibers for imaging, spectroscopy, and beyond}, journal = {Adv. Opt. Photon.}, volume = {15}, year = {2023}, month = {Jun}, pages = {524{\textendash}612}, keywords = {{\textquoteright}KF{\textquoteright}, {\textquoteright}MF{\textquoteright}}, doi = {10.1364/AOP.484298}, url = {https://opg.optica.org/aop/abstract.cfm?URI=aop-15-2-524}, author = {Hui Cao and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and Sergey Turtaev and Tom{\'a}{\v s} Tyc and Stefan Rotter} } @article {3755, title = {Cooling the optical-spin driven limit cycle oscillations of a levitated gyroscope}, journal = {Commun. Phys.}, volume = {6}, year = {2023}, month = {Nov}, pages = {238}, keywords = {LF, MF}, author = {Yoshihiko Arita and Stephen H. Simpson and Graham D. Bruce and Ewan M. Wright and Pavel Zem{\'a}nek and Kishan Dholakia} } @article {3808, title = {Downsizing the Channel Length of Vertical Organic Electrochemical Transistors}, journal = {ACS Applied Materials \& Interfaces}, volume = {15}, year = {2023}, note = {

PMID: 37216209

}, pages = {27002-27009}, keywords = {{\textquoteright}KF{\textquoteright}, {\textquoteright}MF{\textquoteright}}, doi = {10.1021/acsami.3c02049}, url = {https://doi.org/10.1021/acsami.3c02049}, author = {Brodsk{\'y}, Jan and Gablech, Imrich and Migliaccio, Ludovico and Havl{\'\i}{\v c}ek, Marek and Donahue, Mary J. and G{\l}owacki, Eric D.} } @article {3810, title = {Downsizing the Channel Length of Vertical Organic Electrochemical Transistors}, journal = {ACS APPLIED MATERIALS \& INTERFACES}, volume = {15}, year = {2023}, month = {MAY 22}, pages = {27002-27009}, type = {Article}, abstract = {

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.

}, keywords = {KF, MF}, issn = {1944-8244}, doi = {10.1021/acsami.3c02049}, author = {Brodsk{\'y}, Jan and Gablech, Imrich and Migliaccio, Ludovico and Havli{\textquoteright}cek, Marek and Donahue, Mary J. J. and Glowacki, Eric D. D.} } @article {3773, title = {Identification of staphyloxanthin and derivates in yellow-pigmented Staphylococcus capitis subsp. capitis}, journal = {Frontiers in Microbiology}, volume = {14}, year = {2023}, keywords = {BF, MF}, doi = {10.3389/fmicb.2023.1272734}, url = {https://www.frontiersin.org/articles/10.3389/fmicb.2023.1272734}, author = {Siems, Katharina and Runzheimer, Katharina and Rebro{\v s}ov{\'a}, Katar{\'\i}na and Etzbach, Lara and Auerhammer, Alina and Rehm, Anna and Schwengers, Oliver and {\v S}iler, Martin and Samek, Ota and R{\r u}{\v z}i{\v c}ka, Filip and Moeller, Ralf} } @article {3809, title = {In-situ thermal Raman spectroscopy of single-layer graphene on different substrates}, journal = {Materials Today Communications}, volume = {35}, year = {2023}, pages = {105921}, keywords = {{\textquoteright}BF{\textquoteright}, {\textquoteright}MF{\textquoteright}}, doi = {https://doi.org/10.1016/j.mtcomm.2023.105921}, url = {https://www.sciencedirect.com/science/article/pii/S2352492823006128}, author = {Luk{\'a}{\v s} Pr{\r u}cha and Michael Lejeune and Martin Kizovsk{\'y} and Eli{\v s}ka Materna-Mikmekov{\'a}} } @article {3632, title = {Laser-based techniques: Novel tools for the identification and characterization of aged microplastics with developed biofilm}, journal = {Chemosphere}, volume = {313}, year = {2023}, pages = {137373}, abstract = {

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.

}, keywords = {BF, MF}, issn = {0045-6535}, doi = {https://doi.org/10.1016/j.chemosphere.2022.137373}, url = {https://www.sciencedirect.com/science/article/pii/S0045653522038668}, author = {Pavel Po{\v r}{\'\i}zka and Lukas Brunnbauer and Michaela Porkert and Ula Rozman and Gregor Marolt and Daniel Holub and Martin Kizovsk{\'y} and Mark{\'e}ta Bene{\v s}ov{\'a} and Ota Samek and Andreas Limbeck and Jozef Kaiser and Gabriela Kal{\v c}{\'\i}kov{\'a}} } @article {3787, title = {Physiological and transcriptome profiling of Chlorella sorokiniana: A study on azo dye wastewater decolorization}, journal = {Journal of Hazardous Materials}, volume = {460}, year = {2023}, pages = {132450}, abstract = {

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.

}, keywords = {BF, MF}, issn = {0304-3894}, doi = {https://doi.org/10.1016/j.jhazmat.2023.132450}, url = {https://www.sciencedirect.com/science/article/pii/S0304389423017338}, author = {Vladimira Tarbajova and Martina Kolackova and Pavel Chaloupsky and Marketa Dobesova and Petr Capal and Zdenek Pilat and Ota Samek and Pavel Zem{\'a}nek and Pavel Svec and Dagmar Skopalova Sterbova and Marketa Vaculovicova and Lukas Richtera and Alfredo P{\'e}rez-de-Mora and Vojtech Adam and Dalibor Huska} } @article {3729, title = {Rapid Identification of Pathogens Causing Bloodstream Infections by Raman Spectroscopy and Raman Tweezers}, journal = {Microbiology Spectrum}, volume = {11}, year = {2023}, pages = {e00028-23}, keywords = {BF, MF}, doi = {10.1128/spectrum.00028-23}, url = {https://journals.asm.org/doi/abs/10.1128/spectrum.00028-23}, author = {Katar{\'\i}na Rebro{\v s}ov{\'a} and Silvie Bernatov{\'a} and Martin {\v S}iler and Jan Ma{\v s}ek and Ota Samek and Jan Je{\v z}ek and Martin Kizovsk{\'y} and Veronika Hol{\'a} and Pavel Zem{\'a}nek and Filip R{\r u}{\v z}i{\v c}ka} } @article {3796, title = {Rapid identification of pathogens in blood serum via Raman tweezers in combination with advanced processing methods}, journal = {Biomed. Opt. Express}, volume = {14}, year = {2023}, month = {Dec}, pages = {6410{\textendash}6421}, keywords = {AIF, BF, LF, MF}, doi = {10.1364/BOE.503628}, url = {https://opg.optica.org/boe/abstract.cfm?URI=boe-14-12-6410}, author = {Ond{\v r}ej Vacul{\'\i}k and Silvie Bernatov{\'a} and Katar{\'\i}na Rebro{\v s}ov{\'a} and Ota Samek and Luk{\'a}{\v s} {\v S}ilhan and Filip R{\r u} {\v z}i{\v c}ka and Mojm{\'\i}r {\v S}er{\'y} and Martin {\v S}iler and Jan Je{\v z} ek and Pavel Zem{\'a}nek} } @article {3730, title = {Roadmap for optical tweezers}, journal = {Journal of Physics: Photonics}, volume = {5}, year = {2023}, month = {apr}, pages = {022501}, keywords = {LF, MF}, doi = {10.1088/2515-7647/acb57b}, url = {https://dx.doi.org/10.1088/2515-7647/acb57b}, author = {Giovanni Volpe and Onofrio M Marag{\`o} and Halina Rubinsztein-Dunlop and Giuseppe Pesce and Alexander B Stilgoe and Giorgio Volpe and Georgiy Tkachenko and Viet Giang Truong and S{\'\i}le Nic Chormaic and Fatemeh Kalantarifard and Parviz Elahi and Mikael K{\"a}ll and Agnese Callegari and Manuel I Marqu{\'e}s and Antonio A R Neves and Wendel L Moreira and Adriana Fontes and Carlos L Cesar and Rosalba Saija and Abir Saidi and Paul Beck and J{\"o}rg S Eismann and Peter Banzer and Thales F D Fernandes and Francesco Pedaci and Warwick P Bowen and Rahul Vaippully and Muruga Lokesh and Basudev Roy and Gregor Thalhammer-Thurner and Monika Ritsch-Marte and Laura P{\'e}rez Garc{\'\i}a and Alejandro V Arzola and Isaac P{\'e}rez Castillo and Aykut Argun and Till M Muenker and Bart E Vos and Timo Betz and Ilaria Cristiani and Paolo Minzioni and Peter J Reece and Fan Wang and David McGloin and Justus C Ndukaife and Romain Quidant and Reece P Roberts and Cyril Laplane and Thomas Volz and Reuven Gordon and Dag Hanstorp and Javier Tello Marmolejo and Graham D Bruce and Kishan Dholakia and Tongcang Li and Oto Brzobohat{\'y} and Stephen H Simpson and Pavel Zem{\'a}nek and Felix Ritort and Yael Roichman and Valeriia Bobkova and Raphael Wittkowski and Cornelia Denz and G V Pavan Kumar and Antonino Foti and Maria Grazia Donato and Pietro G Gucciardi and Lucia Gardini and Giulio Bianchi and Anatolii V Kashchuk and Marco Capitanio and Lynn Paterson and Philip H Jones and Kirstine Berg-S{\o}rensen and Younes F Barooji and Lene B Oddershede and Pegah Pouladian and Daryl Preece and Caroline Beck Adiels and Anna Chiara De Luca and Alessandro Magazz{\`u} and David Bronte Ciriza and Maria Antonia Iat{\`\i} and Grover A Swartzlander} } @article {3728, title = {SERS-Tags: Selective Immobilization and Detection of Bacteria by Strain-Specific Antibodies and Surface-Enhanced Raman Scattering}, journal = {Biosensors}, volume = {13}, year = {2023}, pages = {182}, keywords = {BF, MF}, issn = {2079-6374}, doi = {10.3390/bios13020182}, url = {https://www.mdpi.com/2079-6374/13/2/182}, author = {Bene{\v s}ov{\'a}, Mark{\'e}ta and Bernatov{\'a}, Silvie and Mika, Filip and Pokorn{\'a}, Zuzana and Je{\v z}ek, Jan and {\v S}iler, Martin and Samek, Ota and R{\r u}{\v z}i{\v c}ka, Filip and Rebro{\v s}ov{\'a}, Katar{\'\i}na and Zem{\'a}nek, Pavel and Pil{\'a}t, Zden{\v e}k} } @article {3803, title = {Stable a-CSi:H films with a wide range of modulus of elasticity and low internal stress}, journal = {Surface and Coatings Technology}, volume = {459}, year = {2023}, pages = {129147}, abstract = {

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{\textendash}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{\textendash}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.

}, keywords = {AIF, MF}, issn = {0257-8972}, doi = {https://doi.org/10.1016/j.surfcoat.2022.129147}, url = {https://www.sciencedirect.com/science/article/pii/S0257897222010684}, author = {Tomas Plichta and Vaclav Sulc and Miloslav Ohlidal and Vladimir Cech} } @article {3754, title = {Synchronization of spin-driven limit cycle oscillators optically levitated in vacuum}, journal = {Nature Communications}, volume = {14}, year = {2023}, pages = {5441}, keywords = {LF, MF}, doi = {10.1038/s41467-023-41129-5}, url = {https://doi.org/10.1038/s41467-023-41129-5}, author = {Brzobohat{\'y}, Oto and Ducha{\v n}, Martin and J{\'a}kl, Petr and Je{\v z}ek, Jan and {\v S}iler, Martin and Zem{\'a}nek, Pavel and Simpson, Stephen H.} } @article {3806, title = {Synthesis of thin-film materials using nonthermal plasma at a higher degree of dissociation}, journal = {Plasma Processes and Polymers}, volume = {20}, year = {2023}, pages = {2300019}, keywords = {{\textquoteright}LF{\textquoteright}, {\textquoteright}MF{\textquoteright}}, doi = {https://doi.org/10.1002/ppap.202300019}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ppap.202300019}, author = {{\v C}ech, Vladim{\'\i}r and Branecky, Martin} } @article {3631, title = {Absolute frequencies of H13C14N hydrogen cyanide transitions in the 1.5-{\textmu}m region with the saturated spectroscopy and a sub-kHz scanning laser}, journal = {Opt. Lett.}, volume = {47}, year = {2022}, month = {Nov}, pages = {5704{\textendash}5707}, abstract = {

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{\textquoteright} center frequencies of the H13C14N isotope in the range from 1526 nm to 1566 nm with 1.3\&\#x00A0;{\texttimes}\&\#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{\textquoteright} resolution compared to the previous result.

}, keywords = {BF, MF}, doi = {10.1364/OL.467633}, url = {https://opg.optica.org/ol/abstract.cfm?URI=ol-47-21-5704}, author = {Jan Hrabina and Martin Hosek and Simon Rerucha and Martin Cizek and Zdenek Pilat and Massimo Zucco and Josef Lazar and Ondrej Cip} } @article {3606, title = {All-optical sub-Kelvin sympathetic cooling of a levitated microsphere in vacuum}, journal = {Optica}, volume = {9}, year = {2022}, month = {Sep}, pages = {1000{\textendash}1002}, abstract = {

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.

}, keywords = {LF, MF}, doi = {10.1364/OPTICA.466337}, url = {https://opg.optica.org/optica/abstract.cfm?URI=optica-9-9-1000}, author = {Y. Arita and G. D. Bruce and E. M. Wright and S. H. Simpson and P. Zem{\'a}nek and K. Dholakia} } @article {3545, title = {Challenges on optical printing of colloidal nanoparticles}, journal = {J. Chem. Phys.}, volume = {156}, year = {2022}, month = {JAN 21}, pages = {034201}, keywords = {LF, MF}, issn = {0021-9606}, doi = {10.1063/5.0078454}, author = {Violi, Ianina L. and Martinez, Luciana P. and Barella, Mariano and Zaza, Cecilia and Chv{\'a}tal, Lukas and Zem{\'a}nek, Pavel and Gutierrez, Marina V. and Paredes, Maria Y. and Scarpettini, Alberto F. and Olmos-Trigo, Jorge and Pais, Valeria R. and Noblega, Ivan Diaz and Cort{\`e}s, Emiliano and Saenz, Juan Jose and Bragas, Andrea V. and Gargiulo, Juli{\`a}n and Stefani, Fernando D.} } @article {3503, title = {Endoscopic Imaging Using a Multimode Optical Fibre Calibrated with Multiple Internal References}, journal = {Photonics}, volume = {9}, year = {2022}, pages = {37}, keywords = {BF, KF, MF}, doi = {10.3390/photonics9010037}, url = {https://www.mdpi.com/2304-6732/9/1/37}, author = {J{\'a}kl, Petr and {\v S}iler, Martin and Je{\v z}ek, Jan and Cifuentes, Angel and Tr{\"a}g{\r a}rdh, Johanna and Zem{\'a}nek, Pavel and Cizmar, Tomas} } @article {3628, title = {Experimental analysis of microhardness changes of subsurface areas affected by WEDM}, journal = {Proceedings of the Institution of Mechanical Engineers, Part E: Journal of Process Mechanical Engineering}, volume = {236}, year = {2022}, pages = {1979-1991}, abstract = {

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.

}, keywords = {AIF, MF}, doi = {10.1177/09544089221078383}, url = {https://doi.org/10.1177/09544089221078383}, author = {Katerina Mouralova and Stefan Michna and Radim Zahradnicek and Josef Bednar and Tomas Plichta and Jiri Fries} } @article {3574, title = {Glycogen, poly(3-hydroxybutyrate) and pigment accumulation in three Synechocystis strains when exposed to a stepwise increasing salt stress}, journal = {JOURNAL OF APPLIED PHYCOLOGY}, volume = {34}, year = {2022}, month = {JUN}, pages = {1227-1241}, keywords = {BF, MF}, issn = {0921-8971}, doi = {10.1007/s10811-022-02693-3}, author = {Meixner, K. and Daffert, C. and Dalnodar, D. and Mrazova, K. and Hrubanov{\'a}, K. and Krzyzanek, V and Nebes{\'a}{\v r}ov{\'a}, J. and Samek, O. and Sedrlova, Z. and Slaninov{\'a}, E. and Sedl{\'a}{\v c}ek, P. and Obru{\v c}a, S. and Fritz, I} } @article {3644, title = {How to Build the {\textquoteleft}{\textquoteleft}Optical Inverse{\textquoteright}{\textquoteright} of a Multimode Fibre}, journal = {Intelligent Computing}, volume = {2022}, year = {2022}, pages = {9816026}, keywords = {KF, MF}, isbn = {null}, doi = {10.34133/2022/9816026}, url = {https://doi.org/10.34133/2022/9816026}, author = {Butaite, Une G. and Kupianskyi, Hlib and Cizmar, Tomas and Phillips, David B.} } @article {3600, title = {Hybrid multimode - multicore fibre based holographic endoscope for deep-tissue neurophotonics}, journal = {Light: Advanced Manufacturing}, volume = {3}, year = {2022}, pages = {1}, keywords = {KF, MF}, issn = {2689-9620}, doi = {10.37188/lam.2022.029}, url = {https://www.light-am.com//article/id/5e7e4e57-462a-4c48-92ca-1aec395fed59}, author = {Yang Du and Sergey Turtaev and Ivo T Leite and Adrian Lorenz and Jens Kobelke and Katrin Wondraczek and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r} } @article {3589, title = {In Vivo Contrast Imaging of Rat Heart with Carbon Dioxide Foam}, journal = {SENSORS}, volume = {22}, year = {2022}, month = {JUL}, pages = {5124}, keywords = {BF, MF}, doi = {10.3390/s22145124}, author = {Karalko, Anton and Kesa, Peter and Jelinek, Frantisek and Sefc, Ludek and Je{\v z}ek, Jan and Zem{\'a}nek, Pavel and Grus, Tomas} } @article {3599, title = {A method for single particle tracking through a multimode fiber}, journal = {Opt. Express}, volume = {30}, year = {2022}, month = {Sep}, pages = {36055{\textendash}36064}, keywords = {KF, MF}, doi = {10.1364/OE.470111}, url = {http://opg.optica.org/oe/abstract.cfm?URI=oe-30-20-36055}, author = {Angel Cifuentes and Johanna Tr{\"a}g{\r a}rdh} } @article {3564, title = {Near perfect focusing through multimode fibres}, journal = {Opt. Express}, volume = {30}, year = {2022}, month = {Mar}, pages = {10645{\textendash}10663}, keywords = {KF, MF}, doi = {10.1364/OE.452145}, url = {http://opg.optica.org/oe/abstract.cfm?URI=oe-30-7-10645}, author = {Andr{\'e} D. Gomes and Sergey Turtaev and Yang Du and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r} } @article {3565, title = {Neurophotonic tools for microscopic measurements and manipulation: status report}, journal = {Neurophotonics}, volume = {9}, year = {2022}, keywords = {KF, MF}, doi = {10.1117/1.NPh.9.S1.013001}, url = {https://doi.org/10.1117/1.NPh.9.S1.013001}, author = {Ahmed Abdelfattah and Sapna Ahuja and Taner Akkin and Srinivasa Rao Allu and David A. Boas and Joshua Brake and Erin M. Buckley and Robert E. Campbell and Anderson I. Chen and Xiaojun Cheng and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and Irene Costantini and Massimo De Vittorio and Anna Devor and Patrick R. Doran and Mirna El Khatib and Valentina Emiliani and Natalie Fomin-Thunemann and Yeshaiahu Fainman and Tom{\'a}s Fern{\'a}ndez Alfonso and Christopher G. L. Ferri and Ariel Gilad and Xue Han and Andrew Harris and Elizabeth M. C. Hillman and Ute Hochgeschwender and Matthew G. Holt and Na Ji and Kivilcim Kili{\c c} and Evelyn M. R. Lake and Lei Li and Tianqi Li and Philipp M{\"a}chler and Rickson C. Mesquita and Evan W. Miller and K.M. Naga Srinivas Nadella and U. Valentin N{\"a}gerl and Yusuke Nasu and Axel Nimmerjahn and Petra Ondr{\'a}{\v c}kov{\'a} and Francesco S. Pavone and Citlali Perez Campos and Darcy S. Peterka and Filippo Pisano and Ferruccio Pisanello and Francesca Puppo and Bernardo L. Sabatini and Sanaz Sadegh and Sava Sakad{\v z}ic and Shy Shoham and Sanaya N. Shroff and R. Angus Silver and Ruth R. Sims and Spencer L. Smith and Vivek J. Srinivasan and Martin Thunemann and Lei Tian and Lin Tian and Thomas Troxler and Antoine Valera and Alipasha Vaziri and Sergei A. Vinogradov and Flavia Vitale and Lihong V. Wang and Hana Uhl{\'\i}{\v r}ov{\'a} and Chris Xu and Changhuei Yang and Mu-Han Yang and Gary Yellen and Ofer Yizhar and Yongxin Zhao} } @article {3576, title = {The potential of combining laser-induced breakdown spectroscopy and Raman spectroscopy data for the analysis of wood samples}, journal = {Spectrochimica Acta Part B: Atomic Spectroscopy}, volume = {195}, year = {2022}, pages = {106487}, abstract = {

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.

}, keywords = {BF, MF}, issn = {0584-8547}, doi = {https://doi.org/10.1016/j.sab.2022.106487}, url = {https://www.sciencedirect.com/science/article/pii/S0584854722001318}, author = {Daniel Holub and Pavel Po{\v r}{\'\i}zka and Martin Kizovsk{\'y} and David Prochazka and Ota Samek and Josef Kaiser} } @article {3629, title = {Production of precision slots in copper foil using micro EDM}, journal = {Scientific Reports}, volume = {12}, year = {2022}, month = {MAR 23}, pages = {5023}, keywords = {AIF, MF}, issn = {2045-2322}, doi = {10.1038/s41598-022-08957-9}, author = {Mouralova, Katerina and Bednar, Josef and Benes, Libor and Plichta, Tom{\'a}{\v s} and Prokes, Tomas and Fries, Jiri} } @article {3575, title = {Raman Spectroscopy-A Novel Method for Identification and Characterization of Microbes on a Single-Cell Level in Clinical Settings}, journal = {FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY}, volume = {12}, year = {2022}, month = {APR 22}, pages = {866463}, keywords = {BF, MF}, issn = {2235-2988}, doi = {10.3389/fcimb.2022.866463}, author = {Rebro{\v s}ov{\'a}, Katar{\'\i}na and Samek, Ota and Kizovsk{\'y}, Martin and Bernatov{\'a}, Silvie and Hol{\'a}, Veronika and R{\r u}{\v z}i{\v c}ka, Filip} } @article {3504, title = {Raman spectroscopy{\textemdash}a tool for rapid differentiation among microbes causing urinary tract infections}, journal = {Analytica Chimica Acta}, volume = {1191}, year = {2022}, pages = {339292}, keywords = {BF, KF, MF}, issn = {0003-2670}, doi = {https://doi.org/10.1016/j.aca.2021.339292}, url = {https://www.sciencedirect.com/science/article/pii/S0003267021011181}, author = {Katar{\'\i}na Rebro{\v s}ov{\'a} and Silvie Bernatov{\'a} and Martin {\v S}iler and Magdalena Uhlirova and Ota Samek and Jan Je{\v z}ek and Veronika Hol{\'a} and Filip R{\r u}{\v z}i{\v c}ka and Pavel Zem{\'a}nek} } @article {3627, title = {Roadmap on wavefront shaping and deep imaging in complex media}, journal = {Journal of Physics: Photonics}, volume = {4}, year = {2022}, month = {aug}, pages = {042501}, abstract = {

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.

}, keywords = {KF, MF}, doi = {10.1088/2515-7647/ac76f9}, url = {https://dx.doi.org/10.1088/2515-7647/ac76f9}, author = {Sylvain Gigan and Ori Katz and Hilton B de Aguiar and Esben Ravn Andresen and Alexandre Aubry and Jacopo Bertolotti and Emmanuel Bossy and Dorian Bouchet and Joshua Brake and Sophie Brasselet and Yaron Bromberg and Hui Cao and Thomas Chaigne and Zhongtao Cheng and Wonshik Choi and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and Meng Cui and Vincent R Curtis and Hugo Defienne and Matthias Hofer and Ryoichi Horisaki and Roarke Horstmeyer and Na Ji and Aaron K LaViolette and Jerome Mertz and Christophe Moser and Allard P Mosk and Nicolas C P{\'e}gard and Rafael Piestun and Sebastien Popoff and David B Phillips and Demetri Psaltis and Babak Rahmani and Herv{\'e} Rigneault and Stefan Rotter and Lei Tian and Ivo M Vellekoop and Laura Waller and Lihong Wang and Timothy Weber and Sheng Xiao and Chris Xu and Alexey Yamilov and Changhuei Yang and Hasan Y{\i}lmaz} } @article {3577, title = {The role of polyhydroxyalkanoates in adaptation of Cupriavidus necator to osmotic pressure and high concentration of copper ions}, journal = {International Journal of Biological Macromolecules}, volume = {206}, year = {2022}, pages = {977-989}, abstract = {

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.

}, keywords = {BF, MF}, issn = {0141-8130}, doi = {https://doi.org/10.1016/j.ijbiomac.2022.03.102}, url = {https://www.sciencedirect.com/science/article/pii/S0141813022005712}, author = {Ivana Novackova and Vendula Hrabalova and Eva Slaninova and Petr Sedlacek and Ota Samek and Martin Koller and Vladislav Krzyzanek and Kamila Hrubanova and Katerina Mrazova and Jana Nebesarova and Stanislav Obruca} } @article {3509, title = {Suppression of the Non-Linear Background in a Multimode Fibre CARS Endoscope}, journal = {Biomedical Optics Express}, volume = {13}, year = {2022}, pages = {862{\textendash}864}, keywords = {KF, MF}, issn = {2156-7085}, doi = {10.1364/BOE.450375}, author = {Pik{\'a}lek, Tom{\'a}{\v s} and Stib{\r u}rek, Miroslav and Simpson, Stephen and Cizmar, Tomas and Tr{\"a}g{\r a}rdh, Johanna} } @article {3630, title = {Surface topography affects the nanoindentation data}, journal = {Thin Solid Films}, volume = {745}, year = {2022}, pages = {139105}, abstract = {

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\ {\textmu}m 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).

}, keywords = {AIF, MF}, issn = {0040-6090}, doi = {https://doi.org/10.1016/j.tsf.2022.139105}, url = {https://www.sciencedirect.com/science/article/pii/S0040609022000268}, author = {Tomas Plichta and Radim Zahradnicek and Vladimir Cech} } @article {3486, title = {The Adhesion of Plasma Nanocoatings Controls the Shear Properties of GF/Polyester Composite}, journal = {Polymers}, volume = {13}, year = {2021}, pages = {593}, abstract = {

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{\textperiodcentered}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.

}, keywords = {AIF, MF}, issn = {2073-4360}, doi = {10.3390/polym13040593}, url = {https://www.mdpi.com/2073-4360/13/4/593}, author = {Plichta, Tom{\'a}{\v s} and {\v S}irjovov{\'a}, Veronika and Zvonek, Milan and Kalinka, Gerhard and {\v C}ech, Vladim{\'\i}r} } @article {3480, title = {An aerogel-based photocatalytic microreactor driven by light guiding for degradation of toxic pollutants}, journal = {Chemical Engineering Journal}, volume = {409}, year = {2021}, month = {APR 1}, pages = {128108}, keywords = {LF, MF}, issn = {1385-8947}, doi = {10.1016/j.cej.2020.128108}, author = {Ozbakir, Yaprak and Jonas, Alexandr and Kiraz, Alper and Erkey, Can} } @article {3435, title = {All-optical manipulation of photonic membranes}, journal = {Opt. Express}, volume = {29}, year = {2021}, month = {May}, pages = {14260{\textendash}14268}, abstract = {

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.

}, keywords = {KF, MF}, doi = {10.1364/OE.420364}, url = {http://www.opticsexpress.org/abstract.cfm?URI=oe-29-10-14260}, author = {Meisam Askari and Blair C. Kirkpatrick and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and Andrea Di Falco} } @article {3436, title = {Compressively sampling the optical transmission matrix of a multimode fibre}, journal = {LIGHT-SCIENCE \& APPLICATIONS}, volume = {10}, year = {2021}, month = {APR 21}, pages = {88}, keywords = {KF, MF}, issn = {2047-7538}, doi = {10.1038/s41377-021-00514-9}, author = {Li, Shuhui and Saunders, Charles and Lum, Daniel J. and Murray-Bruce, John and Goyal, Vivek K. and Cizmar, Tomas and Phillips, David B.} } @article {3479, title = {Computational image enhancement of multimode fibre-based holographic endo-microscopy: harnessing the muddy modes}, journal = {Opt. Express}, volume = {29}, year = {2021}, month = {Nov}, pages = {38206{\textendash}38220}, keywords = {KF, MF}, doi = {10.1364/OE.434848}, url = {http://www.osapublishing.org/oe/abstract.cfm?URI=oe-29-23-38206}, author = {Tereza Tu{\v c}kov{\'a} and Martin {\v S}iler and DE Boonzajer Flaes and Petr J{\'a}kl and Sergey Turtaev and Stanislav Kr{\'a}tk{\'y} and Rainer Heintzmann and Hana Uhl{\'\i}{\v r}ov{\'a} and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r} } @article {3470, title = {Memory effect assisted imaging through multimode optical fibres}, journal = {Nature Communications}, volume = {12}, year = {2021}, pages = {3751}, abstract = {

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 {\textquoteleft}quasi-radial{\textquoteright} 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.

}, keywords = {KF, MF}, issn = {2041-1723}, doi = {10.1038/s41467-021-23729-1}, url = {https://doi.org/10.1038/s41467-021-23729-1}, author = {Li, Shuhui and Horsley, Simon A. R. and Tyc, Tom{\'a}{\v s} and Cizmar, Tomas and Phillips, David B.} } @article {3437, title = {Observing distant objects with a multimode fiber-based holographic endoscope}, journal = {APL Photonics}, volume = {6}, year = {2021}, pages = {036112}, keywords = {KF, MF}, doi = {10.1063/5.0038367}, url = {https://doi.org/10.1063/5.0038367}, author = {Leite,Ivo T. and Turtaev,Sergey and Boonzajer Flaes,Dirk E. and {\v C}i{\v z}m{\'a}r,Tom{\'a}{\v s}} } @article {3481, title = {Optically transportable optofluidic microlasers with liquid crystal cavities tuned by the electric field}, journal = {ACS Applied Materials \& Interfaces}, volume = {13}, year = {2021}, month = {OCT 21}, pages = {50657-50667}, keywords = {BF, LF, MF}, doi = {10.1021/acsami.1c11936}, author = {Jonas, Alexandr and Pil{\'a}t, Zden{\v e}k and Je{\v z}ek, Jan and Bernatov{\'a}, Silvie and Jedli{\v c}ka, Petr and Aas, Mehdi and Kiraz, Alper and Zem{\'a}nek, Pavel} } @article {3450, title = {Polarization-resolved second-harmonic generation imaging through a multimode fiber}, journal = {Optica}, volume = {8}, year = {2021}, pages = {1065{\textendash}1074}, keywords = {KF, MF}, author = {Cifuentes, Angel and Pik{\'a}lek, Tom{\'a}{\v s} and Ondr{\'a}{\v c}kov{\'a}, Petra and Amezcua-Correa, Rodrigo and Antonio-Lopez, Jos{\'e} Enrique and Cizmar, Tomas and Tr{\"a}g{\r a}rdh, Johanna} } @article {3459, title = {The potential of SERS as an AST methodology in clinical settings}, journal = {NANOPHOTONICS}, volume = {10}, year = {2021}, month = {AUG}, pages = {2537-2561}, keywords = {BF, MF}, issn = {2192-8606}, doi = {10.1515/nanoph-2021-0095}, author = {Samek, Ota and Bernatov{\'a}, Silvie and Dohnal, Fadi} } @article {3417, title = {Raman Microspectroscopic Analysis of Selenium Bioaccumulation by Green Alga Chlorella vulgaris}, journal = {Biosensors}, volume = {11}, year = {2021}, pages = {115}, keywords = {BF, MF}, issn = {2079-6374}, doi = {10.3390/bios11040115}, url = {https://www.mdpi.com/2079-6374/11/4/115}, author = {Kizovsk{\'y}, Martin and Pil{\'a}t, Zden{\v e}k and Mylenko, Mykola and Hrouzek, Pavel and Kuta, Jan and Skoup{\'y}, Radim and Krzy{\v z}{\'a}nek, Vladislav and Hrubanov{\'a}, Kamila and Adamczyk, Olga and Je{\v z}ek, Jan and Bernatov{\'a}, Silvie and Klementov{\'a}, Tereza and Gjevik, Al{\v z}b{\v e}ta and {\v S}iler, Martin and Samek, Ota and Zem{\'a}nek, Pavel} } @article {3410, title = {Rapid detection of antibiotic sensitivity of Staphylococcus aureus by Raman tweezers}, journal = {Eur. Phys. J. Plus}, volume = {136}, year = {2021}, pages = {233}, keywords = {BF, KF, MF}, doi = {10.1140/epjp/s13360-021-01152-1}, url = {https://doi.org/10.1140/epjp/s13360-021-01152-1}, author = {Bernatov{\'a}, S. and K. Rebro{\v s}ov{\'a} and Pil{\'a}t, Z. and M. {\v S}er{\'y} and Gjevik, A. and Samek, O. and Je{\v z}ek, J. and {\v S}iler, M. and Kizovsk{\'y}, M. and Klementov{\'a}, T. and Hol{\'a}, V. and F. R{\r u}{\v z}i{\v c}ka and Zem{\'a}nek, P.} } @article {3471, title = {Side-view holographic endomicroscopy via a custom-terminated multimode fibre}, journal = {Opt. Express}, volume = {29}, year = {2021}, pages = {23083{\textendash}23095}, abstract = {

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.

}, keywords = {KF, MF}, doi = {10.1364/OE.426235}, url = {http://www.osapublishing.org/oe/abstract.cfm?URI=oe-29-15-23083}, author = {Beatriz M. Silveira and Tom{\'a}{\v s} Pik{\'a}lek and Miroslav Stib{\r u}rek and Petra Ondr{\'a}{\v c}kov{\'a} and Petr J{\'a}kl and Ivo T. Leite and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r} } @article {3416, title = {Stochastic dynamics of optically bound matter levitated in vacuum}, journal = {Optica}, volume = {8}, year = {2021}, month = {Feb}, pages = {220{\textendash}229}, keywords = {LF, MF}, doi = {10.1364/OPTICA.404851}, author = {Vojtech Svak and Jana Flaj{\v s}manov{\'a} and Luk{\'a}{\v s} Chv{\'a}tal and Martin {\v S}iler and Alexandr Jon{\'a}{\v s} and Jan Je{\v z}ek and Stephen H. Simpson and Pavel Zem{\'a}nek and Oto Brzobohat{\'y}} } @article {3478, title = {Stochastic Hopf bifurcations in vacuum optical tweezers}, journal = {Phys. Rev. A}, volume = {104}, year = {2021}, month = {OCT 15}, pages = {043518}, keywords = {LF, MF}, issn = {2469-9926}, doi = {10.1103/PhysRevA.104.043518}, author = {Simpson, Stephen H. and Arita, Yoshihiko and Dholakia, Kishan and Zem{\'a}nek, Pavel} } @article {3497, title = {Thermal stability of wavefront shaping using a DMD as a spatial light modulator}, journal = {Opt. Express}, volume = {29}, year = {2021}, month = {Dec}, pages = {41808{\textendash}41818}, keywords = {KF, MF}, doi = {10.1364/OE.442284}, url = {http://www.osapublishing.org/oe/abstract.cfm?URI=oe-29-25-41808}, author = {Benjamin Rudolf and Yang Du and Sergey Turtaev and Ivo T. Leite and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r} } @article {3469, title = {Time-averaged image projection through a multimode fiber}, journal = {Opt. Express}, volume = {29}, year = {2021}, pages = {28005{\textendash}28020}, abstract = {

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.

}, keywords = {KF, MF}, doi = {10.1364/OE.431842}, url = {http://www.osapublishing.org/oe/abstract.cfm?URI=oe-29-18-28005}, author = {Dirk Boonzajer Flaes and Hana {\v S}tolzov{\'a} and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r} } @article {3498, title = {Time-of-flight 3D imaging through multimode optical fibers}, journal = {Science}, volume = {374}, year = {2021}, pages = {1395-1399}, keywords = {KF, MF}, doi = {10.1126/science.abl3771 URL = https://www.science.org/doi/abs/10.1126/science.abl3771}, author = {Daan Stellinga and David B. Phillips and Simon Peter Mekhail and Adam Selyem and Sergey Turtaev and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and Miles J. Padgett} } @article {3440, title = {T-matrix calculations of spin-dependent optical forces in optically trapped nanowires}, journal = {The European Physical Journal - Plus}, volume = {136}, year = {2021}, month = {JAN 16}, pages = {86}, keywords = {LF, MF}, issn = {2190-5444}, doi = {10.1140/epjp/s13360-020-01057-5}, author = {Polimeno, P. and Iati, M. A. and Boschi, C. Degli Esposti and Simpson, S. H. and Svak, V. and Brzobohat{\'y}, O. and Zem{\'a}nek, P. and Marago, O. M. and Saija, R.} } @article {3460, title = {The Use of Raman Spectroscopy to Monitor Metabolic Changes in Stressed Metschnikowia sp. Yeasts}, journal = {Microorganisms}, volume = {9}, year = {2021}, pages = {277}, abstract = {

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.

}, keywords = {BF, MF}, issn = {2076-2607}, doi = {10.3390/microorganisms9020277}, url = {https://www.mdpi.com/2076-2607/9/2/277}, author = {N{\v e}mcov{\'a}, Andrea and Gonov{\'a}, Dominika and Samek, Ota and Sipiczki, Matthias and Breierov{\'a}, Emilia and M{\'a}rov{\'a}, Ivana} } @article {3482, title = {Use of Waste Substrates for the Lipid Production by Yeasts of the Genus Metschnikowia{\textemdash}Screening Study}, journal = {Microorganisms}, volume = {9}, year = {2021}, pages = {2295}, abstract = {

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{\textquoteright}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.

}, keywords = {BF, MF}, issn = {2076-2607}, doi = {10.3390/microorganisms9112295}, url = {https://www.mdpi.com/2076-2607/9/11/2295}, author = {N{\v e}mcov{\'a}, Andrea and Szotkowski, Martin and Samek, Ota and Cag{\'a}{\v n}ov{\'a}, Linda and Sipiczki, Matthias and M{\'a}rov{\'a}, Ivana} } @article {3337, title = {Analysis of bacteriophage-host interaction by Raman tweezers}, journal = {Analytical Chemistry}, volume = {92}, year = {2020}, pages = {12304{\textendash}12311}, keywords = {BF, KF, MF}, author = {Pil{\'a}t, Z and Jon{\'a}{\v s}, A and Pil{\'a}tov{\'a}, J and Klementov{\'a}, T and Bernatov{\'a}, S and {\v S}iler, M and Ma{\v n}ka, T and Kizovsk{\'y}, M and R{\r u}{\v z}i{\v c}ka, F and Pan{\r u}{\v c}ek, R and Neugebauer, U and Samek, O and Zem{\'a}nek, P} } @article {3327, title = {Cellular locomotion using environmental topography}, journal = {Nature}, volume = {582}, year = {2020}, pages = {582{\textendash}585}, keywords = {KF, MF}, author = {Anne Reversat and Florian Gaertner and Jack Merrin and Julian Stopp and Saren Tasciyan and Juan Aguilera and Ingrid de Vries and Robert Hauschild and Miroslav Hons and Matthieu Piel and Andrew Callan-Jones and Raphael Voituriez and Michael Sixt} } @article {3367, title = {Coherent oscillations of a levitated birefringent microsphere in vacuum driven by nonconservative rotation-translation coupling}, journal = {Science Advances}, volume = {6}, year = {2020}, keywords = {LF, MF}, author = {Arita, Y and Simpson, SH and Zem{\'a}nek, P and Dholakia, K} } @article {3363, title = {Complex colloidal structures with non-linear optical properties formed in an optical trap}, journal = {Opt. Express}, volume = {28}, year = {2020}, pages = {37700{\textendash}37707}, keywords = {LF, MF}, author = {Oto Brzobohat{\'y} and Luk{\'a}{\v s} Chv{\'a}tal and Martin {\v S}iler and Pavel Zem{\'a}nek} } @article {3368, title = {Entropy Production in an Elementary, Light Driven Micro-Machine}, journal = {Frontiers in Physics}, volume = {8}, year = {2020}, pages = {538}, abstract = {

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.

}, keywords = {KF, LF, MF}, issn = {2296-424X}, doi = {10.3389/fphy.2020.593122}, url = {https://www.frontiersin.org/article/10.3389/fphy.2020.593122}, author = {Box, Stuart J. and Allen, Michael P. and Phillips, David B. and Simpson, Stephen H.} } @article {3326, title = {Nanovortex-driven all-dielectric optical diffusion boosting and sorting concept for lab-on-a-chip platforms}, journal = {Advanced Science}, volume = {7}, year = {2020}, keywords = {LF, MF}, doi = {10.1002/advs.201903049}, author = {Valero, AC and Kislov, D and Gurvitz, EA and Shamkhi, HK and Pavlov, AA and Redka, D and Yankin, S and Zem{\'a}nek, P and Shalin, AS} } @article {3364, title = {Size-based sorting of emulsion droplets in microfluidic channels patterned with laser-ablated guiding tracks}, journal = {Analytical Chemistry}, volume = {92}, year = {2020}, pages = {2597{\textendash}2604}, keywords = {LF, MF}, author = {Rehman, AU and Coskun, UC and Rashid, Z and Morova, B and Jon{\'a}{\v s}, A and Erten, A and Kiraz, A} } @article {3335, title = {Using the transient trajectories of an optically levitated nanoparticle to characterize a stochastic Duffing oscillator}, journal = {Scientific Reports}, volume = {10}, year = {2020}, pages = {14436}, keywords = {LF, MF}, author = {Flaj{\v s}manov{\'a}, Jana and {\v S}iler, Martin and Jedli{\v c}ka, Petr and Hrub{\'y}, Franti{\v s}ek and Brzobohat{\'y}, Oto and Filip, Radim and Zem{\'a}nek, Pavel} } @article {3187, title = {Controlled Oil/Water Partitioning of Hydrophobic Substrates Extending the Bioanalytical Applications of Droplet-Based Microfluidics}, journal = {Anal. Chem.}, volume = {91}, year = {2019}, pages = {10008-10015}, keywords = {BF, MF}, doi = {10.1021/acs.analchem.9b01839}, author = {Bury{\v s}ka, T. and Va{\v s}ina, M. and Gielen, F. and Va{\v n}{\'a}{\v c}ek, P. and van Vliet, L. and Je{\v z}ek, J. and Pil{\'a}t, Z. and Zem{\'a}nek, P. and Damborsk{\'y}, J. and Hollfelder, F. and Prokop, Z.} } @article {3105, title = {The effects of the treatment conditions on the dissolution profile of ethylcellulose coated pellets}, journal = {Europ. J. of Pharmaceutical Sci.}, volume = {132}, year = {2019}, pages = {86-95}, keywords = {BF, MF}, doi = {10.1016/j.ejps.2019.02.034}, author = {Pavlokov{\'a}, S. and Mu{\v s}el{\'\i}k, J. and Sabadkov{\'a}, D. and Bernatov{\'a}, S. and Samek, O. and Neumann, D. and Franc, A.} } @article {3189, title = {Identification of ability to form biofilm in Candida parapsilosis and Staphylococcus epidermidis by Raman spectroscopy}, journal = {Future Microbiology}, volume = {14}, year = {2019}, pages = {509-517}, abstract = {

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.

}, keywords = {BF, KF, MF}, doi = {10.2217/fmb-2018-0297}, url = {https://doi.org/10.2217/fmb-2018-0297}, author = {Rebro{\v s}ov{\'a}, Katar{\'\i}na and {\v S}iler, Martin and Samek, Ota and R{\r u}{\v z}i{\v c}ka, Filip and Bernatov{\'a}, Silvie and Je{\v z}ek, Jan and Zem{\'a}nek, Pavel and Hol{\'a}, Veronika} } @article {3191, title = {Label-free CARS microscopy through a multimode fiber endoscope}, journal = {Opt. Express}, volume = {27}, year = {2019}, pages = {30055{\textendash}30066}, abstract = {

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.

}, keywords = {KF, MF}, doi = {10.1364/OE.27.030055}, url = {http://www.opticsexpress.org/abstract.cfm?URI=oe-27-21-30055}, author = {Johanna Tr{\"a}g{\r a}rdh and Tom{\'a}{\v s} Pik{\'a}lek and Mojm{\'\i}r {\v S}er{\'y} and Tobias Meyer and J{\"u}rgen Popp and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r} } @article {3230, title = {Mechanical Contact Spectroscopy: Characterizing Nanoscale Adhesive Contacts via Thermal Forces}, journal = {LANGMUIR}, volume = {35}, year = {2019}, month = {APR 30}, pages = {5809-5820}, keywords = {LF, MF}, issn = {0743-7463}, doi = {10.1021/acs.langmuir.8b04074}, author = {Jonas, Alexandr and Kochanczyk, Martin and Ramirez, Alexandro D. and Speidel, Michael and Florin, Ernst-Ludwig} } @article {3232, title = {Nanobore fiber focus trap with enhanced tuning capabilities}, journal = {Opt. Express}, volume = {27}, year = {2019}, month = {Dec}, pages = {36221{\textendash}36230}, keywords = {KF, MF}, doi = {10.1364/OE.27.036221}, url = {http://www.opticsexpress.org/abstract.cfm?URI=oe-27-25-36221}, author = {Malte Plidschun and Stefan Weidlich and Martin {\v S}iler and Karina Weber and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and Markus A. Schmidt} } @article {DonatoNL19, title = {Optical Trapping, Optical Binding, and Rotational Dynamics of Silicon Nanowires in Counter-Propagating Beams}, journal = {Nano Lett.}, volume = {19}, year = {2019}, pages = {342-352}, keywords = {LF, MF}, doi = {10.1021/acs.nanolett.8b03978}, author = {Donato, Maria G. and Oto Brzobohat{\'y} and S. H. Simpson and Irrera, Alessia and Leonardi, Antonio A. and Lo Faro, Maria J. and Vojtech Svak and Marag{\`o}, Onofrio M. and P. Zem{\'a}nek} } @article { BrzobohatyOL19, title = {Optomechanical properties of optically self-arranged colloidal waveguides}, journal = {Opt. Lett.}, volume = {44}, year = {2019}, pages = {707-710}, keywords = {LF, MF}, doi = {10.1364/OL.44.000707}, author = {Oto Brzobohat{\'y} and Luk{\'a}{\v s} Chv{\'a}tal and P. Zem{\'a}nek} } @article {3229, title = {Passive sorting of emulsion droplets with different interfacial properties using laser-patterned surfaces}, journal = {MICROFLUIDICS AND NANOFLUIDICS}, volume = {23}, year = {2019}, month = {MAY}, pages = {65}, keywords = {LF, MF}, issn = {1613-4982}, doi = {10.1007/s10404-019-2236-8}, author = {Rashid, Zeeshan and Erten, Ahmet and Morova, Berna and Muradoglu, Metin and Jonas, Alexandr and Kiraz, Alper} } @article {3188, title = {Perspective on light-induced transport of particles: from optical forces to phoretic motion}, journal = {Adv. Opt. Photon.}, volume = {11}, year = {2019}, month = {Sep}, pages = {577{\textendash}678}, keywords = {LF, MF}, doi = {10.1364/AOP.11.000577}, url = {http://aop.osa.org/abstract.cfm?URI=aop-11-3-577}, author = {Pavel Zem{\'a}nek and Giorgio Volpe and Alexandr Jon{\'a}{\v s} and Oto Brzobohat{\'y}} } @article { ArzolaSR19, title = {Spin to orbital light momentum conversion visualized by particle trajectory}, journal = {Sci. Rep.}, volume = {9}, year = {2019}, pages = {4127:1-7}, keywords = {LF, MF}, doi = {10.1038/s41598-019-40475-z}, author = {Alejandro V. Arzola and Luk{\'a}{\v s} Chv{\'a}tal and P J{\'a}kl and P. Zem{\'a}nek} } @article { BrzobohatyACSPHOT19, title = {Tunable Soft-Matter Optofluidic Waveguides Assembled by Light}, journal = {ACS Phot.}, volume = {6}, year = {2019}, pages = {403-410}, keywords = {LF, MF}, doi = {10.1021/acsphotonics.8b01331}, author = {Oto Brzobohat{\'y} and Luk{\'a}{\v s} Chv{\'a}tal and A. Jon{\'a}{\v s} and M {\v S}iler and J. Ka{\v n}ka and J Je{\v z}ek and P. Zem{\'a}nek} } @article {3171, title = {Visualizing gravitational Bessel waves}, journal = {Physical Review D}, volume = {100}, year = {2019}, pages = {044050}, keywords = {LF, MF}, author = {Pat{\'a}k, Ale{\v s} and Zouhar, Martin and {\v R}ih{\'a}{\v c}ek, Tom{\'a}{\v s} and Brzobohat{\'y}, Oto and Ger{\v s}l, Jan and Campbell, Anna Charv{\'a}tov{\'a}} } @article {3190, title = {Wavelength dependent characterization of a multimode fibre endoscope}, journal = {Opt. Express}, volume = {27}, year = {2019}, pages = {28239{\textendash}28253}, abstract = {

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.

}, keywords = {KF, MF}, doi = {10.1364/OE.27.028239}, url = {http://www.opticsexpress.org/abstract.cfm?URI=oe-27-20-28239}, author = {Tom{\'a}{\v s} Pik{\'a}lek and Johanna Tr{\"a}g{\r a}rdh and Stephen Simpson and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r} } @article {3104, title = {Wavelength-Dependent Optical Force Aggregation of Gold Nanorods for SERS in a Microfluidic Chip}, journal = {J. Phys. Chem. C}, volume = {123}, year = {2019}, pages = {5608-5615}, keywords = {BF, MF}, doi = {10.1021/acs.jpcc.8b12493}, author = {Bernatov{\'a}, Silvie and Donato, Maria Grazia and Je{\v z}ek, Jan and Pil{\'a}t, Z. and Samek, Ota and Magazzu, Alessandro and Marag{\`o}, Onofrio M. and Zem{\'a}nek, Pavel and Gucciardi, Pietro G.} } @article { SedlacekAMB19, title = {What keeps polyhydroxyalkanoates in bacterial cells amorphous? A derivation from stress exposure experiments}, journal = {Appl. Microbiol. Biotech.}, volume = {103}, number = {4}, year = {2019}, pages = {1905-1917}, keywords = {BF, MF}, doi = {10.1007/s00253-018-09584-z}, author = {P. Sedl{\'a}{\v c}ek and Slaninov{\'a}, E. and Enev, V. and Koller, M. and J. Nebes{\'a}{\v r}ov{\'a} and I. M{\'a}rov{\'a} and K. Hrubanov{\'a} and V. Krzy{\v z}{\'a}nek and O. Samek and S. Obru{\v c}a} } @article { ProchazkaSAB18, title = {Combination of laser-induced breakdown spectroscopy and Raman spectroscopy for multivariate classification of bacteria}, journal = {Spec. Acta Part B}, volume = {139}, year = {2018}, pages = {6-12}, keywords = {BF, MF}, doi = {10.1016/j.sab.2017.11.004}, author = {D. Proch{\'a}zka and M. Mazura and O. Samek and K. Rebro{\v s}ov{\'a} and P. Po{\v r}{\'\i}zka and J. Klus and P. Proch{\'a}zkov{\'a} and J. Novotn{\'y} and K. Novotn{\'y} and J. Kaiser} } @article { PilatSENS18SERS, title = {Detection of chloroalkanes by surface-enhanced raman spectroscopy in microfluidic chips}, journal = {Sensors}, volume = {18}, year = {2018}, pages = {3212}, keywords = {BF, MF}, doi = {10.3390/s18103212}, author = {Z. Pil{\'a}t and Kizovsk{\'y}, M. and J Je{\v z}ek and Kr{\'a}tk{\'y}, S. and Sobota, J. and M {\v S}iler and O. Samek and Bury{\v s}ka, T. and Va{\v n}{\'a}{\v c}ek, P. and Damborsk{\'y}, J. and Prokop, Z. and P. Zem{\'a}nek} } @article {SilerPRL18, title = {Diffusing up the Hill: Dynamics and Equipartition in Highly Unstable Systems}, journal = {Phys. Rev. Lett.}, volume = {121}, year = {2018}, pages = {23601}, keywords = {LF, MF}, doi = {10.1103/PhysRevLett.121.230601}, author = {M {\v S}iler and Ornigotti, L. and Oto Brzobohat{\'y} and P J{\'a}kl and Artem Ryabov and Holubec, V. and P. Zem{\'a}nek and Radim Filip} } @article { DamkovaLSA18, title = {Enhancement of the {\textquoteleft}tractor-beam{\textquoteright} pulling force on an optically bound structure}, journal = {Light: Sci. Appl.}, volume = {7}, year = {2018}, pages = {17135}, keywords = {LF, MF}, doi = {10.1038/lsa.2017.135}, author = {Damkov{\'a}, Jana and Luk{\'a}{\v s} Chv{\'a}tal and J Je{\v z}ek and Oulehla, Jindrich and Oto Brzobohat{\'y} and P. Zem{\'a}nek} } @article {TurtaevLSA18, title = {High-fidelity multimode fibre-based endoscopy for deep brain in vivo imaging}, journal = {Light: Sci. Appl.}, volume = {7}, year = {2018}, pages = {92}, keywords = {KF, MF}, doi = {10.1038/s41377-018-0094-x}, author = {S. Turtaev and I.T. Leite and Altwegg-Boussac, T. and Pakan, J.M.P. and Rochefort, N.L. and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r} } @article { PilatSENS18Ecoli, title = {Microfluidic Cultivation and Laser Tweezers Raman Spectroscopy of E-coli under Antibiotic Stress}, journal = {Sensors}, volume = {18}, year = {2018}, pages = {1623}, keywords = {BF, MF}, doi = {10.3390/s18051623}, author = {Z. Pil{\'a}t and Silva Bernatov{\'a} and J Je{\v z}ek and Kirchhoff, J. and Tannert, A. and Neugebauer, U. and O. Samek and P. Zem{\'a}nek} } @article { HrubanovaSENS18, title = {Monitoring Candida parapsilosis and Staphylococcus epidermidis Biofilms by a Combination of Scanning Electron Microscopy and Raman Spectroscopy}, journal = {Sensors}, volume = {18}, number = {12}, year = {2018}, pages = {4089}, keywords = {BF, MF}, doi = {10.3390/s18124089}, author = {K. Hrubanov{\'a} and V. Krzy{\v z}{\'a}nek and J. Nebes{\'a}{\v r}ov{\'a} and F. R{\r u}{\v z}i{\v c}ka and Z. Pil{\'a}t and O. Samek} } @article {OzbakirRSOS18, title = {A new type of microphotoreactor with integrated optofluidic waveguide based on solid-air nanoporous aerogels}, journal = {Royal Society Open Science}, volume = {5}, year = {2018}, pages = {180802}, keywords = {BF, MF}, doi = {10.1098/rsos.180802}, author = {Ozbakir, Y. and A. Jon{\'a}{\v s} and Alper Kiraz and Erkey, C.} } @article {RashidJLT18, title = {Optofluidic Dye Lasers Based on Holey Fibers: Modeling and Performance Analysis}, journal = {J. Lightwave. Technol.}, volume = {36}, year = {2018}, pages = {4114-4122}, keywords = {BF, MF}, doi = {10.1109/JLT.2018.2860684}, author = {Rashid, Zeeshan and A. Jon{\'a}{\v s} and Buczynski, Ryszard and Alper Kiraz} } @article {RashidASS18, title = {Reversible switching of wetting properties and erasable patterning of polymer surfaces using plasma oxidation and thermal treatment}, journal = {Appl. Surf. Sci.}, volume = {441}, year = {2018}, pages = {841-852}, keywords = {BF, MF}, doi = {10.1016/j.apsusc.2018.02.089}, author = {Rashid, Zeeshan and Atay, Ipek and Soydan, Seren and Yagci, M. Baris and A. Jon{\'a}{\v s} and Yilgor, Emel and Alper Kiraz and Yilgor, Iskender} } @article {FlaesPRL18, title = {Robustness of Light-Transport Processes to Bending Deformations in Graded-Index Multimode Waveguides}, journal = {Phys. Rev. Lett.}, volume = {120}, year = {2018}, pages = {233901:1-5}, keywords = {KF, MF}, doi = {10.1103/PhysRevLett.120.233901}, author = {Flaes, D.E.B. and Stopka, Jan and S. Turtaev and de Boer, J.F. and Tyc, T. and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r} } @article {BalochSAA18, title = {Sensitivity of compositional measurement of high-pressure fluid mixtures using microcantilever frequency response}, journal = {Sensors Actuators A}, volume = {278}, year = {2018}, pages = {111-126}, keywords = {BF, MF}, doi = {/10.1016/j.sna.2018.05.025}, author = {Baloch, Shadi Khan and A. Jon{\'a}{\v s} and Alper Kiraz and Alaca, B. Erdem and Erkey, Can} } @article {Vasquez-LopezLSA18, title = {Subcellular spatial resolution achieved for deep-brain imaging in vivo using a minimally invasive multimode fiber}, journal = {Light: Sci. Appl.}, volume = {7}, year = {2018}, pages = {110}, keywords = {KF, MF}, doi = {10.1038/s41377-018-0111-0}, author = {Vasquez-Lopez, S.A. and Turcotte, R. and Koren, V. and Ploschner, M. and Padamsey, Z. and Booth, M. and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and Emptage, N.J.} } @article { LeiteNP18, title = {Three-dimensional holographic optical manipulation through a high-numerical-aperture soft-glass multimode fibre}, journal = {Nature Photon.}, volume = {12}, year = {2018}, pages = {33{\textendash}39}, keywords = {KF, MF}, doi = {10.1038/s41566-017-0053-8}, author = {I.T. Leite and S. Turtaev and Xin Jiang and M {\v S}iler and Alfred Cuschieri and Philip St. J. Russell and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r} } @article {SvakNC18, title = {Transverse spin forces and non-equilibrium particle dynamics in a circularly polarized vacuum optical trap}, journal = {Nature Commun.}, volume = {9}, year = {2018}, pages = {5453}, keywords = {LF, MF}, doi = {10.1038/s41467-018-07866-8}, author = {Vojtech Svak and Oto Brzobohat{\'y} and M {\v S}iler and P J{\'a}kl and J. Ka{\v n}ka and P. Zem{\'a}nek and S. H. Simpson} } @article { GargiuloACSNano17, title = {Accuracy and Mechanistic Details of Optical Printing of Single Au and Ag Nanoparticles}, journal = {ACS nano}, volume = {11}, number = {10}, year = {2017}, pages = {9678{\textendash}9688}, keywords = {LF, MF}, doi = {10.1021/acsnano.7b04136}, author = {Gargiulo, Juli{\`a}n and Violi, Ianina L and Cerrota, Santiago and Luk{\'a}{\v s} Chv{\'a}tal and Cort{\`e}s, Emiliano and Perassi, Eduardo M and Diaz, Fernando and P. Zem{\'a}nek and Stefani, Fernando D} } @article {RebrosovsaFB17, title = {Differentiation between Staphylococcus aureus and Staphylococcus epidermidis strains using Raman spectroscopy}, journal = {Future Microbiology}, volume = {12}, year = {2017}, pages = {10}, keywords = {BF, MF}, doi = {10.2217/fmb-2016-0224}, author = {K. Rebro{\v s}ov{\'a} and M {\v S}iler and O. Samek and F. R{\r u}{\v z}i{\v c}ka and Silva Bernatov{\'a} and J Je{\v z}ek and P. Zem{\'a}nek and V. Hol{\'a}} } @article { KarasekOL17, title = {Dynamics of an optically bound structure made of particles of unequal sizes}, journal = {Opt. Lett.}, volume = {42}, number = {7}, year = {2017}, pages = {1436-1439}, keywords = {LF, MF}, issn = {0146-9592}, doi = {10.1364/OL.42.001436}, author = {V{\'\i}t{\v e}zslav Kar{\'a}sek and M {\v S}iler and Oto Brzobohat{\'y} and P. Zem{\'a}nek} } @article {PilatSENS17, title = {Effects of Infrared Optical Trapping on Saccharomyces cerevisiae in a Microfluidic System}, journal = {Sensors}, volume = {17}, year = {2017}, pages = {2640}, keywords = {BF, MF}, doi = {10.3390/s17112640}, author = {Z. Pil{\'a}t and A. Jon{\'a}{\v s} and J Je{\v z}ek and P. Zem{\'a}nek} } @article {HrubanovaMM17, title = {Morphological and Production Changes in Planktonic and Biofilm Cells Monitored Using SEM and Raman Spectroscopy}, journal = {Microscopy and Microanalysis}, volume = {23}, year = {2017}, pages = {S1}, keywords = {BF, MF}, doi = {10.1017/S1431927617006456}, author = {K. Hrubanov{\'a} and V. Krzy{\v z}{\'a}nek and O. Samek and R. Skoup{\'y} and M {\v S}iler and J Je{\v z}ek and S. Obru{\v c}a and P. Zem{\'a}nek} } @article { ArzolaPRL17, title = {Omnidirectional Transport in Fully Reconfigurable Two Dimensional Optical Ratchets}, journal = {Phys. Rev. Lett.}, volume = {118}, year = {2017}, pages = {138002}, keywords = {LF, MF}, doi = {10.1103/PhysRevLett.118.138002}, author = {Alejandro V. Arzola and Villasante-Barahona, Mario and Karen Volke-Sep{\'u}lveda and P J{\'a}kl and P. Zem{\'a}nek} } @article { SimpsonNL17, title = {Optical Binding of Nanowires}, journal = {Nano Lett.}, volume = {17}, number = {6}, year = {2017}, pages = {3485-3492}, keywords = {LF, MF}, doi = {10.1021/acs.nanolett.7b00494}, author = {S. H. Simpson and P. Zem{\'a}nek and Marag{\`o}, Onofrio M. and Jones, Philip H. and Hanna, Simon} } @article {ObrucaNB17, title = {The presence of PHB granules in cytoplasm protects non-halophilic bacterial cells against the harmful impact of hypertonic environments}, journal = {New Biotechnol.}, volume = {39}, year = {2017}, pages = {10}, keywords = {BF, MF}, doi = {10.1016/j.nbt.2017.07.008}, author = {S. Obru{\v c}a and P. Sedl{\'a}{\v c}ek and F. Mravec and V. Krzy{\v z}{\'a}nek and J. Nebes{\'a}{\v r}ov{\'a} and O. Samek and D. Ku{\v c}era and Pavla Bene{\v s}ov{\'a} and K. Hrubanov{\'a} and M. Milerov{\'a} and I. M{\'a}rov{\'a}} } @article {RebrosovaSR17, title = {Rapid identification of staphylococci by Raman spectroscopy}, journal = {Sci. Rep.}, volume = {7}, year = {2017}, pages = {14846}, keywords = {BF, MF}, doi = {10.1038/s41598-017-13940-w}, author = {K. Rebro{\v s}ov{\'a} and M {\v S}iler and O. Samek and F. R{\r u}{\v z}i{\v c}ka and S. Bernatov{\'a} and V. Hol{\'a} and J Je{\v z}ek and P. Zem{\'a}nek and J. Sokolov{\'a} and P. Petr{\'a}{\v s}} } @article { JonasJOSAB17, title = {Thermal tuning of spectral emission from optically trapped liquid-crystal droplet resonators}, journal = {J. Opt. Soc. Am. B}, volume = {34}, year = {2017}, pages = {1855-1864}, keywords = {BF, MF}, doi = {10.1364/JOSAB.34.001855}, author = {A. Jon{\'a}{\v s} and Z. Pil{\'a}t and J Je{\v z}ek and Silva Bernatov{\'a} and T. Fo{\v r}t and P. Zem{\'a}nek and Mehdi Aas and Alper Kiraz} } @article { SilerSR17, title = {Thermally induced micro-motion by inflection in optical potential}, journal = {Sci. Rep.}, volume = {7}, year = {2017}, pages = {1697}, keywords = {LF, MF}, issn = {2045-2322}, doi = {10.1038/s41598-017-01848-4}, author = {M {\v S}iler and P J{\'a}kl and Oto Brzobohat{\'y} and Artem Ryabov and Radim Filip and P. Zem{\'a}nek} } @article { MravecFEMSML16, title = {Accumulation of PHA granules in Cupriavidus necator as seen by confocal fluorescence microscopy}, journal = {FEMS Microbiology Letters}, volume = {363}, year = {2016}, pages = {10}, keywords = {MF}, doi = {10.1093/femsle/fnw094}, author = {F. Mravec and S. Obru{\v c}a and V. Krzy{\v z}{\'a}nek and P. Sedl{\'a}{\v c}ek and K. Hrubanov{\'a} and O. Samek and D. Ku{\v c}era and Pavla Bene{\v s}ov{\'a} and J. Nebes{\'a}{\v r}ov{\'a}} } @article { ObrucaPLOSONE16, title = {Accumulation of Poly(3-hydroxybutyrate) Helps Bacterial Cells to Survive Freezing}, journal = {PLoS ONE}, volume = {11}, year = {2016}, pages = {e0157778}, keywords = {MF}, doi = {10.1371/journal.pone.0157778}, author = {S. Obru{\v c}a and P. Sedl{\'a}{\v c}ek and V. Krzy{\v z}{\'a}nek and F. Mravec and K. Hrubanov{\'a} and O. Samek and D. Ku{\v c}era and Pavla Bene{\v s}ov{\'a} and I. M{\'a}rov{\'a}} } @article { BrzobohatyOE16, title = {Chiral particles in the dual-beam optical trap}, journal = {Opt. Express}, volume = {24}, year = {2016}, pages = {26382-26391}, keywords = {MF}, doi = {10.1364/OE.24.026382}, author = {Oto Brzobohat{\'y} and Hernandez, Raul Josue and S. H. Simpson and Mazzulla, Alfredo and Cipparrone, Gabriella and P. Zem{\'a}nek} } @article { SilerOL16, title = {Direct measurement of the temperature profile close to an optically trapped absorbing particle}, journal = {Opt. Lett.}, volume = {41}, year = {2016}, pages = {870-873}, keywords = {MF}, doi = {10.1364/OL.41.000870}, author = {M {\v S}iler and J Je{\v z}ek and P J{\'a}kl and Z. Pil{\'a}t and P. Zem{\'a}nek} } @article { AntognozziNPhys16, title = {Direct measurements of the extraordinary optical momentum and transverse spin-dependent force using a nano-cantilever}, journal = {Nat. Phys.}, volume = {12}, year = {2016}, pages = {731-735}, keywords = {MF}, doi = {10.1038/nphys3732}, author = {Antognozzi, M. and Bermingham, C. R. and Harniman, R. L. and S. H. Simpson and Senior, J. and Hayward, R. and Hoerber, H. and Dennis, M. R. and Bekshaev, A. Y. and Bliokh, K. Y. and Nori, F.} } @article { ObrucaAMB16, title = {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}, journal = {Appl Microbiol Biotechnol}, volume = {100}, year = {2016}, pages = {1365-1376}, keywords = {MF}, doi = {10.1007/s00253-015-7162-4}, author = {S. Obru{\v c}a and P. Sedl{\'a}{\v c}ek and F. Mravec and O. Samek and I. M{\'a}rov{\'a}} } @article { TomoriJOpt16, title = {Holographic Raman tweezers controlled by Multimodal Natural User Interface}, journal = {J. Opt.}, volume = {18}, year = {2016}, pages = {015602:1-9}, keywords = {MF}, doi = {10.1088/2040-8978/18/1/015602}, author = {Z. Tomori and P. Ke{\v s}a and M. Nikorovi{\v c} and J. Ka{\v n}ka and P J{\'a}kl and M. {\v S}er{\'y} and Silva Bernatov{\'a} and E. Valu{\v s}ov{\'a} and M. Antal{\'\i}k and P. Zem{\'a}nek} } @article { HrubanovaMM16, title = {Morphological and Production Changes in Stressed Red Yeasts Monitored Using SEM and Raman Spectroscopy}, journal = {Microscopy and Microanalysis}, volume = {22}, year = {2016}, pages = {S3}, keywords = {MF}, doi = {10.1017/S1431927616006577}, author = {K. Hrubanov{\'a} and O. Samek and A. Haronikov{\'a} and Silva Bernatov{\'a} and P. Zem{\'a}nek and I. M{\'a}rov{\'a} and V. Krzy{\v z}{\'a}nek} } @article { FilipJOpt16, title = {Noise-to-signal transition of a Brownian particle in the cubic potential: I. general theory}, journal = {Journal of Optics}, volume = {18}, number = {6}, year = {2016}, pages = {065401}, keywords = {MF}, doi = {10.1088/2040-8978/18/6/065401}, author = {Radim Filip and P. Zem{\'a}nek} } @article { ZemanekJOpt16, title = {Noise-to-signal transition of a Brownian particle in the cubic potential: II. optical trapping geometry}, journal = {Journal of Optics}, volume = {18}, number = {6}, year = {2016}, pages = {065402}, keywords = {MF}, doi = {10.1088/2040-8978/18/6/065401}, author = {P. Zem{\'a}nek and M {\v S}iler and Oto Brzobohat{\'y} and P J{\'a}kl and Radim Filip} } @article { IrreraNL16, title = {Photonic Torque Microscopy of the Nonconservative Force Field for Optically Trapped Silicon Nanowires}, journal = {Nano Lett.}, volume = {16}, year = {2016}, pages = {4181-4188}, keywords = {MF}, doi = {10.1021/acs.nanolett.6b01059}, author = {Irrera, Alessia and Magazzu, Alessandro and Artoni, Pietro and S. H. Simpson and Hanna, Simon and Jones, Philip H. and Priolo, Francesco and Gucciardi, Pietro Giuseppe and Marag{\`o}, Onofrio M.} } @article { BzdekCS16, title = {Precise, contactless measurement of the surface tension of picolitre aerosol droplets}, journal = {Chem. Sci.}, volume = {7}, year = {2016}, pages = {274-285}, keywords = {MF}, doi = {10.1039/C5SC03184B}, author = {Bzdek, B.R. and Power, R.M. and S. H. Simpson and Reid, J.P. and Royall, C.P.} } @article {SamekSENS16, title = {Quantitative Raman Spectroscopy Analysis of Polyhydroxyalkanoates Produced by Cupriavidus necator H16}, journal = {Sensors}, volume = {16}, year = {2016}, pages = {1808}, keywords = {MF}, doi = {10.3390/s16111808}, author = {O. Samek and S. Obru{\v c}a and M {\v S}iler and P. Sedl{\'a}{\v c}ek and Pavla Bene{\v s}ov{\'a} and D. Ku{\v c}era and I. M{\'a}rov{\'a} and J Je{\v z}ek and Silva Bernatov{\'a} and P. Zem{\'a}nek} } @article { SimpsonPRA16, title = {Synchronization of colloidal rotors through angular optical binding}, journal = {Phys. Rev. A}, volume = {93}, year = {2016}, pages = {023842}, keywords = {MF}, doi = {10.1103/PhysRevA.93.023842}, author = {S. H. Simpson and Luk{\'a}{\v s} Chv{\'a}tal and P. Zem{\'a}nek} } @article { RyabovPRE16, title = {Thermally-induced passage and current of particles in highly unstable optical potential}, journal = {Phys. Rev.E}, volume = {16}, year = {2016}, pages = {042108}, keywords = {MF}, doi = {10.1103/PhysRevE.94.042108}, author = {Artem Ryabov and P. Zem{\'a}nek and Radim Filip} } @article {BaranekOE15, title = {Aberration resistant axial localization using a self-imaging of vortices}, journal = {Opt. Express}, volume = {23}, year = {2015}, pages = {15316{\textendash}15331}, keywords = {MF}, doi = {10.1364/OE.23.015316}, author = {Michal Bar{\'a}nek and Petr Bouchal and M {\v S}iler and Zden{\v e}k Bouchal} } @article { ChvatalOR15, title = {Binding of a pair of Au nanoparticles in a wide Gaussian standing wave}, journal = {Opt. Rev.}, volume = {22}, year = {2015}, pages = {157-161}, keywords = {MF}, doi = {10.1007/s10043-015-0027-3}, author = {Luk{\'a}{\v s} Chv{\'a}tal and Oto Brzobohat{\'y} and P. Zem{\'a}nek} } @article { BrzobohatyOE15b, title = {Complex rotational dynamics of multiple spheroidal particles in a circularly polarized, dual beam trap}, journal = {Opt. Express}, volume = {23}, year = {2015}, pages = {7273-7287}, keywords = {MF}, doi = {10.1364/OE.23.007273}, author = {Oto Brzobohat{\'y} and Alejandro V. Arzola and M {\v S}iler and Luk{\'a}{\v s} Chv{\'a}tal and P J{\'a}kl and S. H. Simpson and P. Zem{\'a}nek} } @article { KrzyzanekMM15, title = {Cryo-SEM and Raman Spectroscopy Study of the Involvement of Polyhydroxyalkanoates in Stress Response of Bacteria}, journal = {Microscopy and Microanalysis}, volume = {21}, number = {S3}, year = {2015}, pages = {183-184}, keywords = {MF}, doi = {10.1017/S1431927615001713}, author = {V. Krzy{\v z}{\'a}nek and K. Hrubanov{\'a} and O. Samek and S. Obru{\v c}a and I. M{\'a}rov{\'a} and Silva Bernatov{\'a} and M {\v S}iler and P. Zem{\'a}nek} } @article { SamekJBO15, title = {Identification of individual biofilm-forming bacterial cells using Raman tweezers}, journal = {J. Biomed. Opt.}, volume = {20}, number = {5}, year = {2015}, keywords = {MF}, doi = {10.1117/1.JBO.20.5.051038}, author = {O. Samek and Silva Bernatov{\'a} and J Je{\v z}ek and M {\v S}iler and M. {\v S}er{\'y} and V. Krzy{\v z}{\'a}nek and K. Hrubanov{\'a} and P. Zem{\'a}nek and V. Hol{\'a} and F. R{\r u}{\v z}i{\v c}ka} } @article { MlynarikovaSENS15, title = {Influence of Culture Media on Microbial Fingerprints Using Raman Spectroscopy}, journal = {Sensors}, volume = {15}, year = {2015}, pages = {29635-29647}, keywords = {MF}, doi = {10.3390/s151129635}, author = {K. Mlynarikov{\'a} and O. Samek and Silva Bernatov{\'a} and F. R{\r u}{\v z}i{\v c}ka and J Je{\v z}ek and A. Haronikov{\'a} and M {\v S}iler and P. Zem{\'a}nek and V. Hol{\'a}} } @article { HrubanovaMM15, title = {Monitoring of Multilayered Bacterial Biofilm Morphology by Cryo-SEM for Raman Spectroscopy Measurements}, journal = {Microscopy and Microanalysis}, volume = {21}, year = {2015}, pages = {187-188}, keywords = {MF}, doi = {10.1017/S1431927615001737}, author = {K. Hrubanov{\'a} and Silva Bernatov{\'a} and O. Samek and M. {\v S}er{\'y} and P. Zem{\'a}nek and J. Nebes{\'a}{\v r}ov{\'a} and F. R{\r u}{\v z}i{\v c}ka and V. Krzy{\v z}{\'a}nek} } @article { BrzobohatyOE15, title = {Non-spherical gold nanoparticles trapped in optical tweezers: shape matters}, journal = {Opt. Express}, volume = {23}, year = {2015}, pages = {8179-8189}, keywords = {MF}, doi = {10.1364/OE.23.008179}, author = {Oto Brzobohat{\'y} and M {\v S}iler and J. Trojek and Luk{\'a}{\v s} Chv{\'a}tal and V{\'\i}t{\v e}zslav Kar{\'a}sek and P. Zem{\'a}nek} } @article { SilerJQSRT15, title = {Optical trapping in secondary maxima of focused laser beam}, journal = {J. Quant. Spectrosc. Radiat. Transf.}, volume = {162}, year = {2015}, pages = {114 - 121}, keywords = {MF}, doi = {10.1016/j.jqsrt.2015.03.003}, author = {M {\v S}iler and P. Zem{\'a}nek} } @article { BurdikovaDS15, title = {SEM and Raman Spectroscopy Applied to Biomass Analysis for Application in the Field of Biofuels and Food Industry}, journal = {Dairy Sci. Technol.}, volume = {95}, year = {2015}, pages = {687-700}, keywords = {MF}, doi = {10.1007/s13594-015-0253-2}, author = {Z. Burdikov{\'a} and Z. Svindrych and C. Hickey and M. G. Wilkinson and M. A. E. Auty and O. Samek and Silva Bernatov{\'a} and V. Krzy{\v z}{\'a}nek and A. Periasamy and J. J. Sheehan} } @article { SamekMM15, title = {SEM and Raman Spectroscopy Applied to Biomass Analysis for Application in the Field of Biofuels and Food Industry}, journal = {Microscopy and Microanalysis}, volume = {21}, year = {2015}, pages = {1775-1776}, keywords = {MF}, doi = {10.1017/S1431927615009654}, author = {O. Samek and A. Haronikov{\'a} and N. Va{\v s}kovicov{\'a} and K. Hrubanov{\'a} and J Je{\v z}ek and I. M{\'a}rov{\'a} and V. Krzy{\v z}{\'a}nek and P. Zem{\'a}nek} } @article { BrzobohatySR15, title = {Three-Dimensional Optical Trapping of a Plasmonic Nanoparticle using Low Numerical Aperture Optical Tweezers}, journal = {Sci. Rep.}, volume = {5}, year = {2015}, pages = {8106}, keywords = {MF}, doi = {10.1038/srep08106}, author = {Oto Brzobohat{\'y} and M {\v S}iler and J. Trojek and Luk{\'a}{\v s} Chv{\'a}tal and V{\'\i}t{\v e}zslav Kar{\'a}sek and Ale{\v s} Pat{\'a}k and Zuzana Pokorn{\'a} and Filip Mika and P. Zem{\'a}nek} } @article { BoxPRE15, title = {Transitional behavior in hydrodynamically coupled oscillators}, journal = {Phys. Rev. E}, volume = {91}, year = {2015}, pages = {022916}, keywords = {MF}, doi = {10.1103/PhysRevE.91.022916}, author = {S. Box and L. Debono and D. B. Phillips and S. H. Simpson} } @article {PorizkaSENS14, title = {Algal Biomass Analysis by Laser-Based Analytical Techniques{\textemdash}A Review}, journal = {Sensors}, volume = {14}, year = {2014}, pages = {17725-17752}, keywords = {MF}, doi = {10.3390/s140917725}, author = {Po{\v r}{\'\i}zka, P. and P. Proch{\'a}zkov{\'a} and D. Proch{\'a}zka and Sl{\'a}dkov{\'a}, L. and Novotn{\'y}, J. and Petrilak, M. and Brada, M. and O. Samek and Pil{\'a}t, Z. and P. Zem{\'a}nek and Adam, V. and Kizek, R. and Novotn{\'y}, J. and Kaiser, J.} } @article { SamekIJMC14, title = {Candida parapsilosis Biofilm Identification by Raman Spectroscopy}, journal = {Int. J. Mol. Sci.}, volume = {15}, year = {2014}, pages = {23924-23935}, keywords = {MF}, doi = {10.3390/ijms151223924}, author = {O. Samek and K. Mlynarikov{\'a} and Silva Bernatov{\'a} and J Je{\v z}ek and V. Krzy{\v z}{\'a}nek and M {\v S}iler and P. Zem{\'a}nek and F. R{\r u}{\v z}i{\v c}ka and V. Hol{\'a} and M. Mahelov{\'a}} } @article { JaklOE14, title = {Optical sorting of nonspherical and living microobjects in moving interference structures}, journal = {Opt. Express}, volume = {22}, year = {2014}, pages = {29746-29760}, keywords = {MF}, doi = {10.1364/OE.22.029746}, author = {P J{\'a}kl and Alejandro V. Arzola and M {\v S}iler and Luk{\'a}{\v s} Chv{\'a}tal and Karen Volke-Sep{\'u}lveda and P. Zem{\'a}nek} } @article { ArzolaOE14, title = {Rotation, oscillation and hydrodynamic synchronization of optically trapped oblate spheroidal microparticles}, journal = {Opt. Express}, volume = {22}, year = {2014}, pages = {16207-16221}, keywords = {MF}, doi = {10.1364/OE.22.016207}, author = {Alejandro V. Arzola and P J{\'a}kl and Luk{\'a}{\v s} Chv{\'a}tal and P. Zem{\'a}nek} } @article { ArzolaPRE13, title = {Dynamical analysis of an optical rocking ratchet: Theory and experiment}, journal = {Phys. Rev. E}, volume = {87}, year = {2013}, pages = {062910:1-9}, keywords = {MF}, doi = {10.1103/PhysRevE.87.062910}, author = {Alejandro V. Arzola and Karen Volke-Sep{\'u}lveda and Mateos, Jose L.} } @article { BrzobohatyNP13, title = {Experimental demonstration of optical transport, sorting and self-arrangement using a {\textquoteleft}tractor beam{\textquoteright}}, journal = {Nature Photon.}, volume = {7}, number = {2}, year = {2013}, pages = {123-127}, keywords = {MF}, doi = {10.1038/nphoton.2012.332}, author = {Oto Brzobohat{\'y} and V{\'\i}t{\v e}zslav Kar{\'a}sek and M {\v S}iler and Luk{\'a}{\v s} Chv{\'a}tal and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and P. Zem{\'a}nek} } @article { BernatovaMol13, title = {Following the mechanisms of bacteriostatic versus bacericidal action using Raman spectroscopy}, journal = {Molecules}, volume = {18}, year = {2013}, pages = {13188-13199}, keywords = {MF}, doi = {10.3390/molecules181113188}, author = {Silva Bernatov{\'a} and O. Samek and Z. Pil{\'a}t and M. {\v S}er{\'y} and J Je{\v z}ek and P J{\'a}kl and M {\v S}iler and V. Krzy{\v z}{\'a}nek and P. Zem{\'a}nek and V. Hol{\'a} and M. Dvo{\v r}{\'a}{\v c}kov{\'a} and F. R{\r u}{\v z}i{\v c}ka} } @article { TomoriOPJ13, title = {Holographic Raman tweezers controlled by hand gestures and voice commands}, journal = {Optics and Photonics Journal}, volume = {3}, year = {2013}, pages = {331-336}, keywords = {MF}, doi = {10.4236/opj.2013.32B076}, author = {Z. Tomori and M. Antal{\'\i}k and P. Ke{\v s}a and J. Ka{\v n}ka and P J{\'a}kl and M. {\v S}er{\'y} and Silva Bernatov{\'a} and P. Zem{\'a}nek} } @article { SilerJQSRT13, title = {Metallic nanoparticles in a standing wave: optical force and heating}, journal = {J. Quant. Spectrosc. Radiat. Transf.}, volume = {126}, year = {2013}, pages = {84-90}, keywords = {MF}, doi = {10.1016/j.jqsrt.2012.10.005}, author = {M {\v S}iler and Luk{\'a}{\v s} Chv{\'a}tal and P. Zem{\'a}nek} } @article { SilerJQSRT13b, title = {Optical forces in a non-diffracting vortex beam}, journal = {J. Quant. Spectrosc. Radiat. Transf.}, volume = {126}, year = {2013}, pages = {78-83}, keywords = {MF}, doi = {10.1016/j.jqsrt.2012.08.030}, author = {M {\v S}iler and P. Zem{\'a}nek} } @article { BrzobohatyOL13, title = {Optical manipulation of aerosol droplets using a holographic dual and single beam trap}, journal = {Opt. Lett.}, volume = {38}, number = {22}, year = {2013}, pages = {4601-4604}, keywords = {MF}, doi = {10.1364/OL.38.004601}, author = {Oto Brzobohat{\'y} and M {\v S}iler and J Je{\v z}ek and P J{\'a}kl and P. Zem{\'a}nek} } @article { PilatJPPB13, title = {Optical trapping of microalgae at 735{\textendash}1064 nm: Photodamage assessment}, journal = {J. Photochem. Photobiol. B}, volume = {121}, year = {2013}, pages = {27 - 31}, keywords = {MF}, doi = {10.1016/j.jphotobiol.2013.02.006}, author = {Z. Pil{\'a}t and J Je{\v z}ek and M. {\v S}er{\'y} and M. Trt{\'\i}lek and L. Nedbal and P. Zem{\'a}nek} } @article {AasOE13, title = {Spectral tuning of lasing emission from optofluidic droplet microlasers using optical stretching}, journal = {Opt. Express}, volume = {21}, number = {18}, year = {2013}, pages = {21380-21394}, keywords = {MF}, doi = {10.1364/OE.21.021380}, author = {Mehdi Aas and A. Jon{\'a}{\v s} and Alper Kiraz and Oto Brzobohat{\'y} and J Je{\v z}ek and Z. Pil{\'a}t and P. Zem{\'a}nek} } @article {PorizkaSAB12, title = {Application of laser-induced breakdown spectroscopy to the analysis of algal biomass for industrial biotechnology}, journal = {Spectrochim. Acta B}, volume = {74-75}, year = {2012}, pages = {169-176}, keywords = {MF}, doi = {10.1016/j.sab.2012.06.014}, author = {P. Po{\v r}{\'\i}zka and D. Proch{\'a}zka and Z. Pil{\'a}t and Kraj{\v c}arov{\'a}, L. and J. Kaiser and Malina, R. and J. Novotn{\'y} and P. Zem{\'a}nek and J Je{\v z}ek and M. {\v S}er{\'y} and Silva Bernatov{\'a} and V. Krzy{\v z}{\'a}nek and Dobransk{\'a}, K. and K. Novotn{\'y} and M. Trt{\'\i}lek and O. Samek} } @article { TrojekJOSAA12, title = {Optical alignment and confinement of an ellipsoidal nanorod in optical tweezers: a theoretical study}, journal = {J. Opt. Soc. Am. A}, volume = {29}, number = {7}, year = {2012}, pages = {1224{\textendash}1236}, keywords = {MF}, doi = {10.1364/JOSAA.29.001224}, author = {J. Trojek and Luk{\'a}{\v s} Chv{\'a}tal and P. Zem{\'a}nek} } @article { SilerOE12, title = {Optical forces induced behavior of a particle in a non-diffracting vortex beam}, journal = {Opt. Express}, volume = {20}, year = {2012}, pages = {24304-24319}, keywords = {MF}, doi = {10.1364/OE.20.024304}, author = {M {\v S}iler and P J{\'a}kl and Oto Brzobohat{\'y} and P. Zem{\'a}nek} } @article { PilatJAP2012, title = {Raman microspectroscopy of algal lipid bodies: beta-carotene quantification}, journal = {J. Appl. Phycol.}, volume = {24}, year = {2012}, pages = {541-546}, keywords = {MF}, doi = {10.1007/s10811-011-9754-4}, author = {Z. Pil{\'a}t and Silva Bernatov{\'a} and J Je{\v z}ek and M. {\v S}er{\'y} and O. Samek and P. Zem{\'a}nek and L. Nedbal and M. Trt{\'\i}lek} } @article { SilerAPL12, title = {Speed enhancement of multi-particle chain in a traveling standing wave}, journal = {Appl. Phys. Lett.}, volume = {100}, year = {2012}, pages = {051103}, keywords = {MF}, doi = {10.1063/1.3680234}, author = {M {\v S}iler and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and P. Zem{\'a}nek} } @article { SamekLPL11, title = {Characterization of oil-producing microalgae using Raman spectroscopy}, journal = {Laser Phys. Lett.}, volume = {8}, year = {2011}, pages = {701{\textendash}709}, keywords = {MF}, doi = {10.1002/lapl.201110060}, author = {O. Samek and P. Zem{\'a}nek and A. Jon{\'a}{\v s} and Telle, H. H.} } @article { BrzobohatyAPL11, title = {Dynamic size tuning of multidimensional optically bound matter}, journal = {Appl. Phys. Lett.}, volume = {99}, year = {2011}, pages = {101105}, keywords = {MF}, doi = {10.1063/1.3634007}, author = {Oto Brzobohat{\'y} and V{\'\i}t{\v e}zslav Kar{\'a}sek and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and P. Zem{\'a}nek} } @article { CizmarLPL11, title = {The holographic optical micro-manipulation system based on counter-propagating beams}, journal = {Laser Phys. Lett.}, volume = {8}, year = {2011}, pages = {50{\textendash}56}, keywords = {MF}, doi = {10.1002/lapl.201010100}, author = {Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and Oto Brzobohat{\'y} and Kishan Dholakia and P. Zem{\'a}nek} } @article { SilerJOPT11, title = {Parametric study of optical forces acting upon nanoparticles in a single, or a standing, evanescent wave}, journal = {J. Opt.}, volume = {13}, year = {2011}, pages = {044016:1{\textendash}9}, keywords = {MF}, doi = {10.1088/2040-8978/13/4/044016}, author = {M {\v S}iler and P. Zem{\'a}nek} } @article { BrzobohatyOE11, title = {Static and dynamic behavior of two optically bound microparticles in a standing wave}, journal = {Opt. Express}, volume = {19}, year = {2011}, pages = {19613{\textendash}19626}, keywords = {MF}, doi = {10.1364/OE.19.019613}, author = {Oto Brzobohat{\'y} and V{\'\i}t{\v e}zslav Kar{\'a}sek and M {\v S}iler and J. Trojek and P. Zem{\'a}nek} } @article {JonasLA10, title = {Diffusive Mixing of Polymers Investigated by Raman Microspectroscopy and Microrheology}, journal = {Langmuir}, volume = {26}, number = {17}, year = {2010}, pages = {14223-14230}, keywords = {MF}, doi = {10.1021/la101498h}, author = {A. Jon{\'a}{\v s} and De Luca, A. C. and Pesce, G. and Rusciano, G. and A. Sasso and Caserta, S. and Guido, S. and Marrucci, G.} } @article { BrzobohatyOE10, title = {Experimental and theoretical determination of optical binding forces}, journal = {Opt. Express}, volume = {18}, number = {24}, year = {2010}, pages = {25389{\textendash}25402}, keywords = {MF}, issn = {1094-4087}, doi = {10.1364/OE.18.025389}, author = {Oto Brzobohat{\'y} and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and V{\'\i}t{\v e}zslav Kar{\'a}sek and M {\v S}iler and Kishan Dholakia and P. Zem{\'a}nek} } @article { DholakiaRMP10, title = {Gripped by light: Optical binding}, journal = {Rev. Mod. Phys.}, volume = {82}, year = {2010}, pages = {1767{\textendash}1791}, keywords = {MF}, doi = {10.1103/RevModPhys.82.1767}, author = {Kishan Dholakia and P. Zem{\'a}nek} } @article { SilerNJP10, title = {Particle jumps between optical traps in a one-dimensional optical lattice}, journal = {New. J. Phys.}, volume = {12}, year = {2010}, pages = {083001:1{\textendash}20}, keywords = {MF}, doi = {10.1088/1367-2630/12/8/083001}, author = {M {\v S}iler and P. Zem{\'a}nek} } @article { SamekLPL10, title = {The potential of Raman spectroscopy for the identification of biofilm formation by Staphylococcus epidermidis}, journal = {Laser Phys. Lett.}, volume = {7}, year = {2010}, pages = {378{\textendash}383}, type = {Article}, keywords = {MF}, doi = {10.1002/lapl.200910154}, author = {O. Samek and Al-Marashi, J. F. M. and Telle, H. H.} } @article { Samek2010, title = {Raman Microspectroscopy of Individual Algal Cells: Sensing Unsaturation of Storage Lipids in vivo}, journal = {Sensors}, volume = {10}, year = {2010}, pages = {8635{\textendash}8651}, keywords = {MF}, doi = {10.3390/s100908635}, author = {O. Samek and A. Jon{\'a}{\v s} and Z. Pil{\'a}t and P. Zem{\'a}nek and L. Nedbal and T{\v r}{\'\i}ska, J. and Kotas, P. and M. Trt{\'\i}lek} } @article { BartschCPC09, title = {Detecting Sequential Bond Formation Using Three-Dimensional Thermal Fluctuation Analysis}, journal = {Chem. Phys. Chem.}, volume = {10}, number = {9-10, SI}, year = {2009}, pages = {1541-1547}, keywords = {MF}, doi = {10.1002/cphc.200900211}, author = {Bartsch, Tobias F. and Fisinger, Samo and Kochanczyk, Martin D. and Huang, Rongxin and A. Jon{\'a}{\v s} and Florin, Ernst-Ludwig} } @article { PinyuPRL09, title = {Direct Measurement of the Nonconservative Force Field Generated by Optical Tweezers}, journal = {Phys. Rev. Lett.}, volume = {103}, year = {2009}, pages = {108101}, keywords = {MF}, doi = {10.1103/PhysRevLett.103.108101}, author = {Wu, Pinyu and Huang, Rongxin and Tischer, Christian and A. Jon{\'a}{\v s} and Florin, Ernst-Ludwig} } @article { TrojekOE09, title = {Extreme axial optical force in a standing wave achieved by optimized object shape}, journal = {Opt. Express}, volume = {17}, number = {13}, year = {2009}, pages = {10472{\textendash}10488}, publisher = {OSA}, keywords = {MF}, doi = {10.1364/OE.17.010472}, author = {J. Trojek and V{\'\i}t{\v e}zslav Kar{\'a}sek and P. Zem{\'a}nek} } @article { KarasekJOPA09, title = {Longitudinal optical binding of several spherical particles studied by the coupled dipole method}, journal = {J. Opt. A: Pure Appl. Opt.}, volume = {11}, year = {2009}, pages = {034009}, keywords = {MF}, doi = {10.1088/1464-4258/11/3/034009}, author = {V{\'\i}t{\v e}zslav Kar{\'a}sek and Oto Brzobohat{\'y} and P. Zem{\'a}nek} } @article { BrzobohatyOE08, title = {High quality quasi-Bessel beam generated by round-tip axicon}, journal = {Opt. Express}, volume = {16}, year = {2008}, pages = {12688{\textendash}12700}, keywords = {MF}, doi = {10.1364/OE.16.012688}, author = {Oto Brzobohat{\'y} and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and P. Zem{\'a}nek} } @article { JonasEPH08, title = {Light at work: The use of optical forces for particle manipulation, sorting, and analysis.}, journal = {Electophoresis}, volume = {29}, year = {2008}, pages = {4813{\textendash}4851}, keywords = {MF}, doi = {10.1002/elps.200800484}, author = {A. Jon{\'a}{\v s} and P. Zem{\'a}nek} } @article { KarasekPRL08, title = {Long-range one-dimensional longitudinal optical binding}, journal = {Phys. Rev. Lett.}, volume = {101}, number = {14}, year = {2008}, pages = {143601}, keywords = {MF}, issn = {0031-9007}, doi = {10.1103/PhysRevLett.101.143601}, author = {V{\'\i}t{\v e}zslav Kar{\'a}sek and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and Oto Brzobohat{\'y} and P. Zem{\'a}nek and V. Garc{\'e}s-Ch{\'a}vez and Kishan Dholakia} } @article { JaklAPL08, title = {Static optical sorting in a laser interference field}, journal = {Appl. Phys. Lett.}, volume = {92}, number = {16}, year = {2008}, pages = {161110:1{\textendash}3}, keywords = {MF}, issn = {0003-6951}, doi = {10.1063/1.2913759}, author = {P J{\'a}kl and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and M. {\v S}er{\'y} and P. Zem{\'a}nek} } @article { SilerNJP08, title = {Surface delivery of a single nanoparticle under moving evanescent standing-wave illumination}, journal = {New. J. Phys.}, volume = {10}, year = {2008}, pages = {113010}, keywords = {MF}, issn = {1367-2630}, doi = {10.1088/1367-2630/10/11/113010}, author = {M {\v S}iler and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and A. Jon{\'a}{\v s} and P. Zem{\'a}nek} } @article { KarasekJOPA07, title = {Analytical description of longitudinal optical binding of two spherical nanoparticles}, journal = {J. Opt. A: Pure Appl. Opt.}, volume = {9}, year = {2007}, pages = {S215{\textendash}S220}, keywords = {MF}, doi = {10.1088/1464-4258/9/8/S14}, author = {V{\'\i}t{\v e}zslav Kar{\'a}sek and P. Zem{\'a}nek} } @article { JaklJOPAA07, title = {Axial optical trap stiffness influenced by retro-reflected beam}, journal = {J. Opt. A: Pure Appl. Opt.}, volume = {9}, number = {8, Sp. Iss. SI}, year = {2007}, pages = {S251{\textendash}S255}, keywords = {MF}, issn = {1464-4258}, doi = {10.1088/1464-4258/9/8/S19}, author = {P J{\'a}kl and M. {\v S}er{\'y} and J Je{\v z}ek and M. Li{\v s}ka and P. Zem{\'a}nek} } @article { DholakiaMCB07, title = {Cellular and colloidal separation using optical forces}, journal = {Methods in Cell Biology}, volume = {82}, year = {2007}, pages = {467{\textendash}495}, keywords = {MF}, doi = {10.1016/S0091-679X(06)82017-0}, author = {Kishan Dholakia and MacDonald, M. P. and P. Zem{\'a}nek and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r} } @article { SilerOC07, title = {Optical forces acting on a nanoparticle placed into an interference evanescent field}, journal = {Opt. Commun.}, volume = {275}, year = {2007}, pages = {409{\textendash}420}, keywords = {MF}, doi = {10.1016/j.optcom.2007.03.074}, author = {M {\v S}iler and P. Zem{\'a}nek} } @article { CizmarOE07, title = {Optical tracking of spherical micro-objects in spatially periodic interference fields}, journal = {Opt. Express}, volume = {15}, year = {2007}, pages = {2262{\textendash}2272}, keywords = {MF}, doi = {10.1364/OE.15.002262}, author = {Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and P. Zem{\'a}nek} } @article { JaklJOAM07, title = {Opto-fluidic micromanipulation system based on integrated polymer waveguides}, journal = {J. Optoel Adv. Mater.}, volume = {9}, year = {2007}, pages = {2148-2151}, keywords = {MF}, author = {P J{\'a}kl and M. {\v S}er{\'y} and J Je{\v z}ek and P. Zem{\'a}nek and Ormos, P. and Valkai, S. and Kelemen, L.} } @article { MilneOE07, title = {Transverse particle dynamics in a Bessel beam}, journal = {Opt. Express}, volume = {15}, number = {21}, year = {2007}, pages = {13972{\textendash}13987}, publisher = {OSA}, keywords = {MF}, doi = {10.1364/OE.15.013972}, url = {http://www.opticsexpress.org/abstract.cfm?URI=oe-15-21-13972}, author = {Milne, Graham and Kishan Dholakia and McGloin, David and Karen Volke-Sep{\'u}lveda and P. Zem{\'a}nek} } @article {KarasekAPB06, title = {Analysis of optical binding in one dimension}, journal = {Appl. Phys. B}, volume = {84}, year = {2006}, pages = {149{\textendash}156}, keywords = {MF}, doi = {10.1007/s00340-006-2297-8}, author = {V{\'\i}t{\v e}zslav Kar{\'a}sek and Kishan Dholakia and P. Zem{\'a}nek} } @article {JezekOE06, title = {Formation of long and thin polymer fiber using nondiffracting beam}, journal = {Opt. Express}, volume = {14}, year = {2006}, pages = {8506-8515}, keywords = {MF}, doi = {10.1364/OE.14.008506}, author = {J Je{\v z}ek and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and V. Ned{\v e}la and P. Zem{\'a}nek} } @article {SilerAPB06, title = {Optical forces generated by evanescent standing waves and their usage for sub-micron particle delivery}, journal = {Appl. Phys. B}, volume = {84}, year = {2006}, pages = {157{\textendash}165}, keywords = {MF}, doi = {10.1007/s00340-006-2235-9}, author = {M {\v S}iler and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and M. {\v S}er{\'y} and P. Zem{\'a}nek} } @article {CizmarAPB06, title = {An optical nanotrap array movable over a milimetre range}, journal = {Appl. Phys. B}, volume = {84}, year = {2006}, pages = {197{\textendash}203}, keywords = {MF}, doi = {10.1007/s00340-006-2221-2}, author = {Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and M {\v S}iler and P. Zem{\'a}nek} } @article {CizmarPRB06, title = {Optical sorting and detection of sub-micron objects in a motional standing wave}, journal = {Phys. Rev. B}, volume = {74}, year = {2006}, pages = {035105:1-6}, keywords = {MF}, doi = {10.1103/PhysRevB.74.035105}, author = {Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and M {\v S}iler and M. {\v S}er{\'y} and P. Zem{\'a}nek and V. Garc{\'e}s-Ch{\'a}vez and Kishan Dholakia} } @article {CizmarNJP06, title = {Sub-micron particle organization by self-imaging of non-diffracting beams}, journal = {New. J. Phys.}, volume = {8}, year = {2006}, pages = {43}, keywords = {MF}, doi = {10.1088/1367-2630/8/3/043}, author = {Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and V. Koll{\'a}rov{\'a} and Zden{\v e}k Bouchal and P. Zem{\'a}nek} } @article {CizmarAPL05, title = {Optical conveyor belt for delivery of submicron objects}, journal = {Appl. Phys. Lett.}, volume = {86}, year = {2005}, pages = {174101-1{\textendash}174101-3}, keywords = {MF}, doi = {10.1063/1.1915543}, author = {Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and V. Garc{\'e}s-Ch{\'a}vez and Kishan Dholakia and P. Zem{\'a}nek} } @article {CasaburiOC05, title = {Two-and three-beam interferometric optical tweezers}, journal = {Opt. Commun.}, volume = {251}, year = {2005}, pages = {393{\textendash}404}, keywords = {MF}, doi = {10.1016/j.optcom.2005.03.029}, author = {A. Casaburi and G. Pesce and P. Zem{\'a}nek and A. Sasso} } @article {ZemanekOPTCOMM04, title = {Optical forces acting on Rayleigh particle placed into interference field}, journal = {Opt. Commun.}, volume = {240}, year = {2004}, pages = {401-415}, keywords = {MF}, doi = {10.1016/j.optcom.2004.06.051}, author = {P. Zem{\'a}nek and V{\'\i}t{\v e}zslav Kar{\'a}sek and A. Sasso} } @article {JaklJMO03, title = {Behaviour of an optically trapped probe approaching a dielectric interface}, journal = {J Mod. Optics}, volume = {50}, year = {2003}, pages = {1615-1625}, keywords = {MF}, doi = {10.1080/09500340308235235}, author = {P J{\'a}kl and M. {\v S}er{\'y} and J Je{\v z}ek and A. Jon{\'a}{\v s} and M. Li{\v s}ka and P. Zem{\'a}nek} } @article {ZemanekOPTCOMM03, title = {Theoretical comparison of optical traps created by standing wave and single beam}, journal = {Opt. Commun.}, volume = {220}, year = {2003}, pages = {401-412}, keywords = {MF}, doi = {10.1016/S0030-4018(03)01409-3}, author = {P. Zem{\'a}nek and A. Jon{\'a}{\v s} and P J{\'a}kl and M. {\v S}er{\'y} and J Je{\v z}ek and M. Li{\v s}ka} } @article {ZemanekJOSAA02, title = {Simplified description of optical forces acting on a nanoparticle in the Gaussian standing wave}, journal = {J. Opt. Soc. Am. A}, volume = {19}, year = {2002}, pages = {1025-1034}, keywords = {MF}, doi = {10.1364/JOSAA.19.001025}, author = {P. Zem{\'a}nek and A. Jon{\'a}{\v s} and M. Li{\v s}ka} } @article {JonasOL01, title = {Single beam trapping in front of reflective surfaces}, journal = {Opt. Lett.}, volume = {26}, year = {2001}, pages = {1466{\textendash}1468}, keywords = {MF}, doi = {10.1364/OL.26.001466}, author = {A. Jon{\'a}{\v s} and P. Zem{\'a}nek and E. - L. Florin} } @article {ZemanekOL99, title = {Optical trapping of nanoparticles and microparticles using Gaussian standing wave.}, journal = {Opt. Lett.}, volume = {24}, year = {1999}, pages = {1448{\textendash}1450}, keywords = {MF}, doi = {10.1364/OL.24.001448}, author = {P. Zem{\'a}nek and A. 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