Simulation of optomechanical interaction of levitated nanoparticle with photonic crystal micro cavity.

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

Identification of staphyloxanthin and derivates in yellow-pigmented Staphylococcus capitis subsp. capitis.

Introduction: Staphylococcus capitis naturally colonizes the human skin but as an opportunistic pathogen, it can also cause biofilm-associated infections and bloodstream infections in newborns. Previously, we found that two strains from the subspecies S. capitis subsp. capitis produce yellow carotenoids despite the initial species description, reporting this subspecies as non-pigmented. In Staphylococcus aureus, the golden pigment staphyloxanthin is an important virulence factor, protecting cells against reactive oxygen species and modulating membrane fluidity. Methods: In this study, we used two pigmented (DSM 111179 and DSM 113836) and two non-pigmented S. capitis subsp. capitis strains (DSM 20326T and DSM 31028) to identify the pigment, determine conditions under which pigment-production occurs and investigate whether pigmented strains show increased resistance to ROS and temperature stress. Results: We found that the non-pigmented strains remained colorless regardless of the type of medium, whereas intensity of pigmentation in the two pigmented strains increased under low nutrient conditions and with longer incubation times. We were able to detect and identify staphyloxanthin and its derivates in the two pigmented strains but found that methanol cell extracts from all four strains showed ROS scavenging activity regardless of staphyloxanthin production. Increased survival to cold temperatures (-20°C) was detected in the two pigmented strains only after long-term storage compared to the non-pigmented strains. Conclusion: The identification of staphyloxanthin in S. capitis is of clinical relevance and could be used, in the same way as in S. aureus, as a possible target for anti-virulence drug design.

Synchronization of spin-driven limit cycle oscillators optically levitated in vacuum.

We explore, experimentally and theoretically, the emergence of coherent coupled oscillations and synchronization between a pair of non-Hermitian, stochastic, opto-mechanical oscillators, levitated in vacuum. Each oscillator consists of a polystyrene microsphere trapped in a circularly polarized, counter-propagating Gaussian laser beam. Non-conservative, azimuthal forces, deriving from inhomogeneous optical spin, push the micro-particles out of thermodynamic equilibrium. For modest optical powers each particle shows a tendency towards orbital circulation. Initially, their stochastic motion is weakly correlated. As the power is increased, the tendency towards orbital circulation strengthens and the motion of the particles becomes highly correlated. Eventually, centripetal forces overcome optical gradient forces and the oscillators undergo a collective Hopf bifurcation. For laser powers exceeding this threshold, a pair of limit cycles appear, which synchronize due to weak optical and hydrodynamic interactions. In principle, arrays of such Non-Hermitian elements can be arranged, paving the way for opto-mechanical topological materials or, possibly, classical time crystals. In addition, the preparation of synchronized states in levitated optomechanics could lead to new and robust sensors or alternative routes to the entanglement of macroscopic objects.

Aspergillus niger as a cell factory for the production of pyomelanin, a molecule with UV-C radiation shielding activity.

Melanins are complex pigments with various biological functions and potential applications in space exploration and biomedicine due to their radioprotective properties. Aspergillus niger, a fungus known for its high radiation resistance, is widely used in biotechnology and a candidate for melanin production. In this study, we investigated the production of fungal pyomelanin (PyoFun) in A. niger by inducing overproduction of the pigment using L-tyrosine in a recombinant ΔhmgA mutant strain (OS4.3). The PyoFun pigment was characterized using three spectroscopic methods, and its antioxidant properties were assessed using a DPPH-assay. Additionally, we evaluated the protective effect of PyoFun against non-ionizing radiation (monochromatic UV-C) and compared its efficacy to a synthetically produced control pyomelanin (PyoSyn). The results confirmed successful production of PyoFun in A. niger through inducible overproduction. Characterization using spectroscopic methods confirmed the presence of PyoFun, and the DPPH-assay demonstrated its strong antioxidant properties. Moreover, PyoFun exhibited a highly protective effect against radiation-induced stress, surpassing the protection provided by PyoSyn. The findings of this study suggest that PyoFun has significant potential as a biological shield against harmful radiation. Notably, PyoFun is synthesized extracellularly, differing it from other fungal melanins (such as L-DOPA- or DHN-melanin) that require cell lysis for pigment purification. This characteristic makes PyoFun a valuable resource for biotechnology, biomedicine, and the space industry. However, further research is needed to evaluate its protective effect in a dried form and against ionizing radiation.

110 µm thin endo-microscope for deep-brain in vivo observations of neuronal connectivity, activity and blood flow dynamics.

Light-based in-vivo brain imaging relies on light transport over large distances of highly scattering tissues. Scattering gradually reduces imaging contrast and resolution, making it difficult to reach structures at greater depths even with the use of multiphoton techniques. To reach deeper, minimally invasive endo-microscopy techniques have been established. These most commonly exploit graded-index rod lenses and enable a variety of modalities in head-fixed and freely moving animals. A recently proposed alternative is the use of holographic control of light transport through multimode optical fibres promising much less traumatic application and superior imaging performance. We present a 110 µm thin laser-scanning endo-microscope based on this prospect, enabling in-vivo volumetric imaging throughout the whole depth of the mouse brain. The instrument is equipped with multi-wavelength detection and three-dimensional random access options, and it performs at lateral resolution below 1 µm. We showcase various modes of its application through the observations of fluorescently labelled neurones, their processes and blood vessels. Finally, we demonstrate how to exploit the instrument to monitor calcium signalling of neurones and to measure blood flow velocity in individual vessels at high speeds.

Rapid Identification of Pathogens Causing Bloodstream Infections by Raman Spectroscopy and Raman Tweezers.

The search for the "Holy Grail" in clinical diagnostic microbiology-a reliable, accurate, low-cost, real-time, easy-to-use method-has brought up several methods with the potential to meet these criteria. One is Raman spectroscopy, an optical, nondestructive method based on the inelastic scattering of monochromatic light. The current study focuses on the possible use of Raman spectroscopy for identifying microbes causing severe, often life-threatening bloodstream infections. We included 305 microbial strains of 28 species acting as causative agents of bloodstream infections. Raman spectroscopy identified the strains from grown colonies, with 2.8% and 7% incorrectly identified strains using the support vector machine algorithm based on centered and uncentred principal-component analyses, respectively. We combined Raman spectroscopy with optical tweezers to speed up the process and captured and analyzed microbes directly from spiked human serum. The pilot study suggests that it is possible to capture individual microbial cells from human serum and characterize them by Raman spectroscopy with notable differences among different species. IMPORTANCE Bloodstream infections are among the most common causes of hospitalizations and are often life-threatening. To establish an effective therapy for a patient, the timely identification of the causative agent and characterization of its antimicrobial susceptibility and resistance profiles are essential. Therefore, our multidisciplinary team of microbiologists and physicists presents a method that reliably, rapidly, and inexpensively identifies pathogens causing bloodstream infections-Raman spectroscopy. We believe that it might become a valuable diagnostic tool in the future. Combined with optical trapping, it offers a new approach where the microorganisms are individually trapped in a noncontact way by optical tweezers and investigated by Raman spectroscopy directly in a liquid sample. Together with the automatic processing of measured Raman spectra and comparison with a database of microorganisms, it makes the whole identification process almost real time.

SERS-Tags: Selective Immobilization and Detection of Bacteria by Strain-Specific Antibodies and Surface-Enhanced Raman Scattering.

Efficient separation and sensitive identification of pathogenic bacterial strains is essential for a prosperous modern society, with direct applications in medical diagnostics, drug discovery, biodefense, and food safety. We developed a fast and reliable method for antibody-based selective immobilization of bacteria from suspension onto a gold-plated glass surface, followed by detection using strain-specific antibodies linked to gold nanoparticles decorated with a reporter molecule. The reporter molecules are subsequently detected by surface-enhanced Raman spectroscopy (SERS). Such a multi-functionalized nanoparticle is called a SERS-tag. The presented procedure uses widely accessible and cheap materials for manufacturing and functionalization of the nanoparticles and the immobilization surfaces. Here, we exemplify the use of the produced SERS-tags for sensitive single-cell detection of opportunistic pathogen Escherichia coli, and we demonstrate the selectivity of our method using two other bacterial strains, Staphylococcus aureus and Serratia marcescens, as negative controls. We believe that the described approach has a potential to inspire the development of novel medical diagnostic tools for rapid identification of bacterial pathogens.

Rapid identification of pathogens in blood serum via Raman tweezers in combination with advanced processing methods.

Pathogenic microbes contribute to several major global diseases that kill millions of people every year. Bloodstream infections caused by these microbes are associated with high morbidity and mortality rates, which are among the most common causes of hospitalizations. The search for the "Holy Grail" in clinical diagnostic microbiology, a reliable, accurate, low cost, real-time, and easy-to-use diagnostic method, is one of the essential issues in clinical practice. These very critical conditions can be met by Raman tweezers in combination with advanced analysis methods. Here, we present a proof-of-concept study based on Raman tweezers combined with spectral mixture analysis that allows for the identification of microbial strains directly from human blood serum without user intervention, thus eliminating the influence of a data analyst.

Raman spectroscopy-a tool for rapid differentiation among microbes causing urinary tract infections.

Urinary tract infections belong to the most common infections in the world. Besides community-acquired infections, nosocomial infections pose a high risk especially for patients having indwelling catheters, undergoing urological surgeries or staying at hospital for prolonged time. They can be often complicated by antimicrobial resistance and/or biofilm formation. Therefore, a rapid diagnostic tool enabling timely identification of a causative agent and its susceptibility to antimicrobials is a need. Raman spectroscopy appears to be a suitable method that allows rapid differentiation among microbes and provides a space for further analyses, such as determination of capability of biofilm formation or antimicrobial susceptibility/resistance in tested strains. Our work here presents a possibility to differ among most common microbes causing urinary tract infections (belonging to 20 species). We tested 254 strains directly from colonies grown on Mueller-Hinton agar plates. The results show that it is possible to distinguish among the tested species using Raman spectroscopy, which proves its great potential for future use in clinical diagnostics. Moreover, we present here a pilot study of a real-time analysis and identification (in less than 10 min) of single microbial cells directly in urine employing optical tweezers combined with Raman spectroscopy.

Computational image enhancement of multimode fibre-based holographic endo-microscopy: harnessing the muddy modes.

In imaging geometries, which employ wavefront-shaping to control the light transport through a multi-mode optical fibre (MMF), this terminal hair-thin optical component acts as a minimally invasive objective lens, enabling high resolution laser-scanning fluorescence microscopy inside living tissues at depths hardly accessible by any other light-based technique. Even in the most advanced systems, the diffraction-limited foci scanning the object across the focal plane are contaminated by a stray optical signal carrying typically few tens of % of the total optical power. The stray illumination takes the shape of a randomised but reproducible speckle, and is unique for each position of the focus. We experimentally demonstrate that the performance of imaging a fluorescent object can be significantly improved, when resulting images are computationally post-processed, utilising records of intensities of all speckle-contaminated foci used in the imaging procedure. We present two algorithms based on a regularised iterative inversion and regularised direct pseudo-inversion respectively which lead to enhancement of the image contrast and resolution.

Raman Microspectroscopic Analysis of Selenium Bioaccumulation by Green Alga Chlorella vulgaris.

Selenium (Se) is an element with many commercial applications as well as an essential micronutrient. Dietary Se has antioxidant properties and it is known to play a role in cancer prevention. However, the general population often suffers from Se deficiency. Green algae, such as Chlorella vulgaris, cultivated in Se-enriched environment may be used as a food supplement to provide adequate levels of Se. We used Raman microspectroscopy (RS) for fast, reliable, and non-destructive measurement of Se concentration in living algal cells. We employed inductively coupled plasma-mass spectrometry as a reference method to RS and we found a substantial correlation between the Raman signal intensity at 252 cm-1 and total Se concentration in the studied cells. We used RS to assess the uptake of Se by living and inactivated algae and demonstrated the necessity of active cellular transport for Se accumulation. Additionally, we observed the intracellular Se being transformed into an insoluble elemental form, which we further supported by the energy-dispersive X-ray spectroscopy imaging.

Complex colloidal structures with non-linear optical properties formed in an optical trap.

Illumination of a colloidal suspension of dielectric nanoparticles (50 nm in radius) with counter-propagating non-interfering laser beams of sufficient power leads to spatial redistribution of particles due to associated optical forces and formation of colloidal structures composed of thousands of nanoparticles along the beams. We employ a weak probe beam propagating through the colloidal structure and demonstrate that the colloidal structure acts effectively as a non-linear optical medium, similar to a gradient index lens, with optical transformation properties externally tunable by trapping laser power. With an increasing number of nanoparticles we observe the formation of a more complex colloidal structure axially and even laterally and we explain the origin of this process.

Using the transient trajectories of an optically levitated nanoparticle to characterize a stochastic Duffing oscillator.

We propose a novel methodology to estimate parameters characterizing a weakly nonlinear Duffing oscillator represented by an optically levitating nanoparticle. The method is based on averaging recorded trajectories with defined initial positions in the phase space of nanoparticle position and momentum and allows us to study the transient dynamics of the nonlinear system. This technique provides us with the parameters of a levitated nanoparticle such as eigenfrequency, damping, coefficient of nonlinearity and effective temperature directly from the recorded transient particle motion without any need for external driving or modification of an experimental system. Comparison of this innovative approach with a commonly used method based on fitting the power spectrum density profile shows that the proposed complementary method is applicable even at lower pressures where the nonlinearity starts to play a significant role and thus the power spectrum density method predicts steady state parameters. The technique is applicable also at low temperatures and extendable to recent quantum experiments. The proposed method is applied on experimental data and its validity for one-dimensional and three-dimensional motion of a levitated nanoparticle is verified by extensive numerical simulations.

Analysis of Bacteriophage-Host Interaction by Raman Tweezers.

Bacteriophages, or "phages" for short, are viruses that replicate in bacteria. The therapeutic and biotechnological potential of phages and their lytic enzymes is of interest for their ability to selectively destroy pathogenic bacteria, including antibiotic-resistant strains. Introduction of phage preparations into medicine, biotechnology, and food industry requires a thorough characterization of phage-host interaction on a molecular level. We employed Raman tweezers to analyze the phage-host interaction of Staphylococcus aureus strain FS159 with a virulent phage JK2 (=812K1/420) of the Myoviridae family and a temperate phage 80α of the Siphoviridae family. We analyzed the timeline of phage-induced molecular changes in infected host cells. We reliably detected the presence of replicating phages in bacterial cells within 5 min after infection. Our results lay the foundations for building a Raman-based diagnostic instrument capable of real-time, in vivo, in situ, nondestructive characterization of the phage-host relationship on the level of individual cells, which has the potential of importantly contributing to the development of phage therapy and enzybiotics.

Nanobore fiber focus trap with enhanced tuning capabilities.

Confinement in fiber traps with two optical fibers facing one another relies on balancing the optical forces originating from the interaction of a scattering micro-object with the light beams delivered through the fibers. Here we demonstrate a novel type of dual fiber trap that involves the use of nanobore fibers, having a nano-channel located in the center of their fiber cores. This nano-element leads to a profound redistribution of the optical intensity and to considerably higher field gradients, yielding a trapping potential with greatly improved tuning properties compared to standard step-index fiber types. We evaluate the trap performance as a function of the fiber separation and find substantially higher stiffness for the nanobore fiber trap, especially in the range of short inter-fiber separations, while intermediate distances exhibit axial stiffness below that of the standard fiber. The results are in agreement with theoretical predictions and reveal that the exploitation of nanobore fibers allows for combinations of transverse and axial stiffness that cannot be accessed with common step-index fibers.

Identification of ability to form biofilm in Candida parapsilosis and Staphylococcus epidermidis by Raman spectroscopy.

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.

Diffusing up the Hill: Dynamics and Equipartition in Highly Unstable Systems.

Stochastic motion of particles in a highly unstable potential generates a number of diverging trajectories leading to undefined statistical moments of the particle position. This makes experiments challenging and breaks down a standard statistical analysis of unstable mechanical processes and their applications. A newly proposed approach takes advantage of the local characteristics of the most probable particle motion instead of the divergent averages. We experimentally verify its theoretical predictions for a Brownian particle moving near an inflection in a highly unstable cubic optical potential. The most likely position of the particle atypically shifts against the force, despite the trajectories diverging in the opposite direction. The local uncertainty around the most likely position saturates even for strong diffusion and enables well-resolved position detection. Remarkably, the measured particle distribution quickly converges to a quasistationary one with the same atypical shift for different initial particle positions. The demonstrated experimental confirmation of the theoretical predictions approves the utility of local characteristics for highly unstable systems which can be exploited in thermodynamic processes to uncover energetics of unstable systems.

Detection of Chloroalkanes by Surface-Enhanced Raman Spectroscopy in Microfluidic Chips.

Optofluidics, a research discipline combining optics with microfluidics, currently aspires to revolutionize the analysis of biological and chemical samples, e.g., for medicine, pharmacology, or molecular biology. In order to detect low concentrations of analytes in water, we have developed an optofluidic device containing a nanostructured substrate for surface enhanced Raman spectroscopy (SERS). The geometry of the gold surface allows localized plasmon oscillations to give rise to the SERS effect, in which the Raman spectral lines are intensified by the interaction of the plasmonic field with the electrons in the molecular bonds. The SERS substrate was enclosed in a microfluidic system, which allowed transport and precise mixing of the analyzed fluids, while preventing contamination or abrasion of the highly sensitive substrate. To illustrate its practical use, we employed the device for quantitative detection of persistent environmental pollutant 1,2,3-trichloropropane in water in submillimolar concentrations. The developed sensor allows fast and simple quantification of halogenated compounds and it will contribute towards the environmental monitoring and enzymology experiments with engineered haloalkane dehalogenase enzymes.

Rapid identification of staphylococci by Raman spectroscopy.

Clinical treatment of the infections caused by various staphylococcal species differ depending on the actual cause of infection. Therefore, it is necessary to develop a fast and reliable method for identification of staphylococci. Raman spectroscopy is an optical method used in multiple scientific fields. Recent studies showed that the method has a potential for use in microbiological research, too. Our work here shows a possibility to identify staphylococci by Raman spectroscopy. We present a method that enables almost 100% successful identification of 16 of the clinically most important staphylococcal species directly from bacterial colonies grown on a Mueller-Hinton agar plate. We obtained characteristic Raman spectra of 277 staphylococcal strains belonging to 16 species from a 24-hour culture of each strain grown on the Mueller-Hinton agar plate using the Raman instrument. The results show that it is possible to distinguish among the tested species using Raman spectroscopy and therefore it has a great potential for use in routine clinical diagnostics.

Differentiation between Staphylococcus aureus and Staphylococcus epidermidis strains using Raman spectroscopy.

AIM: Raman spectroscopy is an analytical method with a broad range of applications across multiple scientific fields. We report on a possibility to differentiate between two important Gram-positive species commonly found in clinical material - Staphylococcus aureus and Staphylococcus epidermidis - using this rapid noninvasive technique. MATERIALS & METHODS: For this, we tested 87 strains, 41 of S. aureus and 46 of S. epidermidis, directly from colonies grown on a Mueller-Hinton agar plate using Raman spectroscopy. DISCUSSION & CONCLUSION: The method paves a way for separation of these two species even on high number of samples and therefore, it can be potentially used in clinical diagnostics.