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.

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.

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.

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.

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.

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.

Dynamics of an optically bound structure made of particles of unequal sizes.

This theoretical study based on the coupled dipoles model focuses on the dynamics of two optically bound dielectric spheres of unequal sizes confined in counter-propagating incoherent Bessel beams. We analyzed the relative motion of the particles with respect to each other and defined conditions where they form a stable optically bound structure (OBS). We also investigated the motion of the center of mass of the OBS and found that its direction depends on the particle separation in the structure. Besides the optical interaction between objects, we also considered a hydrodynamic coupling in order to obtain more precise results for moving an OBS.

Direct measurement of the temperature profile close to an optically trapped absorbing particle.

The surface temperature of an absorbing particle trapped in optical tweezers (OTs) is measured using a mixture of two fluorescent dyes. We analyze the dependence of temperature on both laser power and the radial distance from its surface, and we verify the 1/r decrease of temperature with increasing distance from the particle surface. We detect the variations of spectral profiles as the medium temperature changes. The temperature dependent signal, i.e., the ratio of summed intensities from two distinct spectral regions, is affected by the convolution of temperature profile with transfer function of the spectroscopic system. We analyze this effect and determine the temperature increase on the surface of a core-shell particle trapped by OTs.

Quantitative Raman Spectroscopy Analysis of Polyhydroxyalkanoates Produced by Cupriavidus necator H16.

We report herein on the application of Raman spectroscopy to the rapid quantitative analysis of polyhydroxyalkanoates (PHAs), biodegradable polyesters accumulated by various bacteria. This theme was exemplified for quantitative detection of the most common member of PHAs, poly(3-hydroxybutyrate) (PHB) in Cupriavidus necator H16. We have identified the relevant spectral region (800-1800 cm-1) incorporating the Raman emission lines exploited for the calibration of PHB (PHB line at 1736 cm-1) and for the selection of the two internal standards (DNA at 786 cm-1 and Amide I at 1662 cm-1). In order to obtain quantitative data for calibration of intracellular content of PHB in bacterial cells reference samples containing PHB amounts-determined by gas chromatography-from 12% to 90% (w/w) were used. Consequently, analytical results based on this calibration can be used for fast and reliable determination of intracellular PHB content during biotechnological production of PHB since the whole procedure-from bacteria sampling, centrifugation, and sample preparation to Raman analysis-can take about 12 min. In contrast, gas chromatography analysis takes approximately 8 h.

Aberration resistant axial localization using a self-imaging of vortices.

The vortex self-imaging (SI) implemented in optical imaging systems and its usage for a robust axial localization of point-like objects are presented. The vortex SI is used to generate a double-helix point spread function (DH PSF) maintaining its shape and size unchanged in a large working area. The robustness of the axial localization is demonstrated by a resistance against the spherical aberration. Using a thorough analysis, the experiments are optimized to achieve the highest localization sensitivity and to find a trade-off between the aberration stability of the DH PSF, the length of the localization range and the energy efficiency. The benefits of the method are achieved by applying the SI of nondiffracting vortices prepared by a spatial light modulator (SLM). The feasibility of the proposed technique is demonstrated by a defocusing induced rotation of the fixed and moving 1µm polystyrene beads, carried out in the transmitted light illumination.

Non-spherical gold nanoparticles trapped in optical tweezers: shape matters.

We present the results of a theoretical analysis focused on three-dimensional optical trapping of non-spherical gold nanoparticles using a tightly focused laser beam (i.e. optical tweezers). We investigate how the wavelength of the trapping beam enhances trapping stiffness and determines the stable orientation of nonspherical nanoparticles in the optical trap which reveals the optimal trapping wavelength. We consider nanoparticles with diameters being between 20 nm and 254 nm illuminated by a highly focused laser beam at wavelength 1064 nm and compare our results based on the coupled-dipole method with published theoretical and experimental data. We demonstrate that by considering the non-spherical morphology of the nanoparticle we can explain the experimentally observed three-dimensional trapping of plasmonic nanoparticles with size higher than 170 nm. These results will contribute to a better understanding of the trapping and alignment of real metal nanoparticles in optical tweezers and their applications as optically controllable nanosources of heat or probes of weak forces and torques.

Complex rotational dynamics of multiple spheroidal particles in a circularly polarized, dual beam trap.

We examine the rotational dynamics of spheroidal particles in an optical trap comprising counter-propagating Gaussian beams of opposing helicity. Isolated spheroids undergo continuous rotation with frequencies determined by their size and aspect ratio, whilst pairs of spheroids display phase locking behaviour. The introduction of additional particles leads to yet more complex behaviour. Experimental results are supported by numerical calculations.

Influence of Culture Media on Microbial Fingerprints Using Raman Spectroscopy.

Raman spectroscopy has a broad range of applications across numerous scientific fields, including microbiology. Our work here monitors the influence of culture media on the Raman spectra of clinically important microorganisms (Escherichia coli, Staphylococcus aureus, Staphylococcus epidermidis and Candida albicans). Choosing an adequate medium may enhance the reproducibility of the method as well as simplifying the data processing and the evaluation. We tested four different media per organism depending on the nutritional requirements and clinical usage directly on a Petri dish. Some of the media have a significant influence on the microbial fingerprint (Roosvelt-Park Institute Medium, CHROMagar) and should not be used for the acquisition of Raman spectra. It was found that the most suitable medium for microbiological experiments regarding these organisms was Mueller-Hinton agar.

Optical sorting of nonspherical and living microobjects in moving interference structures.

Contactless, sterile and nondestructive separation of microobjects or living cells is demanded in many areas of biology and analytical chemistry, as well as in physics or engineering. Here we demonstrate advanced sorting methods based on the optical forces exerted by travelling interference fringes with tunable periodicity controlled by a spatial light modulator. Besides the sorting of spherical particles we also demonstrate separation of algal cells of different sizes and particles of different shapes. The three presented methods offer simultaneous sorting of more objects in static suspension placed in a Petri dish or on a microscope slide.

Candida parapsilosis biofilm identification by Raman spectroscopy.

Colonies of Candida parapsilosis on culture plates were probed directly in situ using Raman spectroscopy for rapid identification of specific strains separated by a given time intervals (up to months apart). To classify the Raman spectra, data analysis was performed using the approach of principal component analysis (PCA). The analysis of the data sets generated during the scans of individual colonies reveals that despite the inhomogeneity of the biological samples unambiguous associations to individual strains (two biofilm-positive and two biofilm-negative) could be made.

Optical manipulation of aerosol droplets using a holographic dual and single beam trap.

We present optical trapping and manipulation of pure water and salt water airborne droplets of various sizes ranging from sub-micrometers up to several tens of micrometers in a holographic dual and single beam trap. In the dual beam trap, successful fusion of droplets as well as precise delivery of many droplets and manipulation of multiple droplets are demonstrated. Furthermore, employing the transfer of the orbital angular momentum of light from Laguerre-Gaussian beams, we show that the water droplets orbit around the beam propagation axis and their tangential speed can be controlled by beam waist magnitude. We also demonstrate that sub-micrometer sized pure water droplets can be trapped and manipulated by a single beam trap with a relatively low numerical aperture. In this case, multiple stable trapping positions were observed, both theoretically and experimentally, which were due to the optical intensity oscillations in the focal region of the laser beam.

Following the mechanisms of bacteriostatic versus bactericidal action using Raman spectroscopy.

Antibiotics cure infections by influencing bacterial growth or viability. Antibiotics can be divided to two groups on the basis of their effect on microbial cells through two main mechanisms, which are either bactericidal or bacteriostatic. Bactericidal antibiotics kill the bacteria and bacteriostatic antibiotics suppress the growth of bacteria (keep them in the stationary phase of growth). One of many factors to predict a favorable clinical outcome of the potential action of antimicrobial chemicals may be provided using in vitro bactericidal/bacteriostatic data (e.g., minimum inhibitory concentrations-MICs). Consequently, MICs are used in clinical situations mainly to confirm resistance, and to determine the in vitro activities of new antimicrobials. We report on the combination of data obtained from MICs with information on microorganisms' "fingerprint" (e.g., DNA/RNA, and proteins) provided by Raman spectroscopy. Thus, we could follow mechanisms of the bacteriostatic versus bactericidal action simply by detecting the Raman bands corresponding to DNA. The Raman spectra of Staphylococcus epidermidis treated with clindamycin (a bacteriostatic agent) indeed show little effect on DNA which is in contrast with the action of ciprofloxacin (a bactericidal agent), where the Raman spectra show a decrease in strength of the signal assigned to DNA, suggesting DNA fragmentation.

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.

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.