Influence of antireflection Si coatings on the damage threshold of fused silica upon irradiation with mid-IR femtosecond laser pulses.

Recent progress in the development of high-power mid-IR laser sources and the exciting laser driven physical phenomena associated with the irradiation of solids via ultrashort laser pulses in that spectral region are aimed to potentially create novel capabilities for material processing. In particular, the investigation of the underlying physical processes and the evaluation of the optical breakdown threshold (OBT) following irradiation of bulk dielectric materials with mid-IR femtosecond (fs) pulses have been recently presented. In this Letter, we will explore the conditions that generate sufficient carrier excitation levels which lead to damage upon irradiation of a dielectric material (SiO2) coated with antireflection (AR) semiconducting films (Si) of variable thickness with fs pulses. Simulation results demonstrate that the reflectivity and transmissivity of the Si/SiO2 are thickness dependent which can be employed to modulate the damage threshold of the substrate. The study is to provide innovative routes for selecting material sizes that can be used for antireflection coatings and applications in the mid-IR region.

Impact of Pre-Patterned Structures on Features of Laser-Induced Periodic Surface Structures.

The efficiency of light coupling to surface plasmon polariton (SPP) represents a very important issue in plasmonics and laser fabrication of topographies in various solids. To illustrate the role of pre-patterned surfaces and impact of laser polarisation in the excitation of electromagnetic modes and periodic pattern formation, Nickel surfaces are irradiated with femtosecond laser pulses of polarisation perpendicular or parallel to the orientation of the pre-pattern ridges. Experimental results indicate that for polarisation parallel to the ridges, laser induced periodic surface structures (LIPSS) are formed perpendicularly to the pre-pattern with a frequency that is independent of the distance between the ridges and periodicities close to the wavelength of the excited SPP. By contrast, for polarisation perpendicular to the pre-pattern, the periodicities of the LIPSS are closely correlated to the distance between the ridges for pre-pattern distance larger than the laser wavelength. The experimental observations are interpreted through a multi-scale physical model in which the impact of the interference of the electromagnetic modes is revealed.

Light driven optofluidic switch developed in a ZnO-overlaid microstructured optical fiber.

A great challenge of Optofluidics remains the control of the fluidic properties of a photonic circuit by solely utilizing light. In this study, the development of a ZnO nanolayered microstructured optical fiber (MOF) Fabry-Perot interferometer is demonstrated, along with its fully reversible optofluidic switching behaviour. The actuation and switching principle is entirely based on the employment of light sources, i.e. UV 248 nm and green 532 nm lasers, while using modest irradiation doses. The synthesized ZnO within the MOF capillaries acts as a light triggered wettability transducer, allowing the controlled water filling and draining of the MOF Fabry-Perot cavity. The progression of the optofluidic cycle is monitored in situ with optical microscopy, while Fabry-Perot reflection spectra are monitored in real time to probe temporal infiltration behaviour. Finally, a first insight on the light triggered switching mechanism, employing photoluminescence and spectrophotometric measurements is presented. Results appear highly promising towards the design of smart in-fiber optofluidic light switching devices, suitable for actuating and sensing applications.

High acoustic strains in Si through ultrafast laser excitation of Ti thin-film transducers.

The role of thin-film metal transducers in ultrafast laser-generated longitudinal acoustic phonons in Si (100) monocrystal substrates is investigated. For this purpose degenerate femtosecond pump-probe transient reflectivity measurements are performed probing the Brillouin scattering of laser photons from phonons. The influence of the metallic electron-phonon coupling factor, acoustical impedance and film thickness is examined. An optical transfer matrix method for thin films is applied to extract the net acoustic strain relative strength for the various transducer cases, taking into account the experimental probing efficiency. In addition, a theoretical thermo-mechanical approach based on the combination of a revised two-temperature model and elasticity theory is applied and supports the experimental findings. The results show highly efficient generation of acoustic phonons in Si when Ti transducers are used. This demonstrates the crucial role of the transducer's high electron-phonon coupling constant and high compressive yield strength, as well as strong acoustical impedance matching with the semiconductor substrate.

Ripple formation on nickel irradiated with radially polarized femtosecond beams.

We report on the morphological effects induced by the inhomogeneous absorption of radially polarized femtosecond laser irradiation of nickel (Ni) in sub-ablation conditions. A theoretical prediction of the morphology profile is performed, and the role of surface plasmon excitation in the production of self-formed periodic ripple structures is evaluated. Results indicate a smaller periodicity of the ripples profile compared to that attained under linearly polarized irradiation conditions. A combined hydrodynamical and thermoelastic model is presented in laser beam conditions that lead to material melting. The simulation results are presented to be in good agreement with the experimental findings. The ability to control the size of the morphological changes via modulating the beam polarization may provide an additional route for controlling and optimizing the outcome of laser micro-processing.

Fabrication of Biomimetic 2D Nanostructures through Irradiation of Stainless Steel Surfaces with Double Femtosecond Pulses.

Femtosecond laser induced changes on the topography of stainless steel with double pulses is investigated to reveal the role of parameters such as the fluence, the energy dose and the interpulse delay on the features of the produced patterns. Our results indicate that short pulse separation (Δτ = 5 ps) favors the formation of 2D Low Spatially Frequency Laser Induced Periodic Surface Structures (LSFL) while longer interpulse delays (Δτ = 20 ps) lead to 2D High Spatially Frequency LIPSS (HSFL). The detailed investigation is complemented with an analysis of the produced surface patterns and characterization of their wetting and cell-adhesion properties. A correlation between the surface roughness and the contact angle is presented which confirms that topographies of variable roughness and complexity exhibit different wetting properties. Furthermore, our analysis indicates that patterns with different spatial characteristics demonstrate variable cell adhesion response which suggests that the methodology can be used as a strategy towards the fabrication of tailored surfaces for the development of functional implants.

Femtosecond Laser-Induced Periodic Surface Structures on 2D Ti-Fe Multilayer Condensates.

2D Ti-Fe multilayer preparation has been attracting increased interest due to its ability to form intermetallic compounds between metallic titanium and metallic iron thin layers. In particular, the TiFe compound can absorb hydrogen gas at room temperature. We applied femtosecond laser pulses to heat Ti-Fe multilayer structures to promote the appearance of intermetallic compounds and generate surface nanostructuring. The surface pattern, known as Laser Induced Periodic Surface Structures (LIPSS), can accelerate the kinetics of chemical interaction between solid TiFe and gaseous hydrogen. The formation of LIPSS on Ti-Fe multilayered thin films were investigated using of scanning electron microscopy, photo-electron spectroscopy and X-ray diffraction. To explore the thermal response of the multiple layered structure and the mechanisms leading to surface patterning after irradiating the compound with single laser pulses, theoretical simulations were conducted to interpret the experimental observations.

Ionisation processes and laser induced periodic surface structures in dielectrics with mid-infrared femtosecond laser pulses.

Irradiation of solids with ultrashort pulses and laser processing in the mid-Infrared (mid-IR) spectral region is a yet predominantly unexplored field with a large potential for a wide range of applications. In this work, laser driven physical phenomena associated with processes following irradiation of fused silica (SiO2) with ultrashort laser pulses in the mid-IR region are investigated in detail. A multiscale modelling approach is performed that correlates conditions for formation of perpendicular or parallel to the laser polarisation low spatial frequency periodic surface structures for low and high intensity mid-IR pulses (not previously explored in dielectrics at those wavelengths), respectively. Results demonstrate a remarkable domination of tunneling effects in the photoionisation rate and a strong influence of impact ionisation for long laser wavelengths. The methodology presented in this work is aimed to shed light on the fundamental mechanisms in a previously unexplored spectral area and allow a systematic novel surface engineering with strong mid-IR fields for advanced industrial laser applications.

Biomimetic Omnidirectional Antireflective Glass via Direct Ultrafast Laser Nanostructuring.

Here, a single-step, biomimetic approach for the realization of omnidirectional transparent antireflective glass is reported. In particular, it is shown that circularly polarized ultrashort laser pulses produce self-organized nanopillar structures on fused silica (SiO2 ). The laser-induced nanostructures are selectively textured on the glass surface in order to mimic the spatial randomness, pillar-like morphology, as well as the remarkable antireflection properties found on the wings of the glasswing butterfly, Greta oto, and various Cicada species. The artificial structures exhibit impressive antireflective properties, both in the visible and infrared frequency ranges, which are remarkably stable over time. Accordingly, the laser-processed glass surfaces show reflectivity smaller than 1% for various angles of incidence in the visible spectrum for s-p linearly polarized configurations. However, in the near-infrared spectrum, the laser-textured glass shows higher transmittance compared to the pristine. It is envisaged that the current results will revolutionize the technology of antireflective transparent surfaces and impact numerous applications from glass displays to optoelectronic devices.

Investigation of binding mechanisms of nuclear proteins using confocal scanning laser microscopy and FRAP.

Fluorescence recovery after photobleaching (FRAP) measurements offer an important tool towards analysing diffusion processes within living biological cells. A model is presented that aims to provide a rigorous theoretical framework from which binding information of proteins from FRAP data can be extracted. A single binding reaction is considered and a set of mathematical equations is introduced that incorporates the concentration of free proteins, vacant binding sites and bound complexes in addition to the on- and off-rates of the proteins. To allow a realistic FRAP model, characteristics of the instruments used to perform FRAP measurements are included in the equation. The proposed model has been designed to be applied to biological samples with a confocal scanning laser microscope (CSLM) equipped with the feature to bleach regions characterised by a radially Gaussian distributed profile. Binding information emerges from FRAP simulations considering the diffusion coefficient, radial extent of the bleached volume and bleach constant as parameters derived from experimental data. The proposed model leads to FRAP curves that depend on the on- and off-rates. Analytical expressions are used to define the boundaries of on- and off-rate parameter space in simplified cases when molecules can move on an infinite domain. A similar approach is ensued when movement is restricted in a compartment with a finite size. The theoretical model can be used in conjunction to experimental data acquired by CSLM to investigate the biophysical properties of proteins in living cells.

Investigation of femtosecond laser induced ripple formation on copper for varying incident angle.

The hydrodynamic mechanisms associated with the formation of femtosecond laser induced ripples on copper for two angles of incidence are reported. Laser pulse length used for this work is 35 fs. A revised two-temperature model is presented that comprises transient changes of optical characteristics during the irradiation with femtosecond pulses to model relaxation processes and thermal response in bulk copper. The theoretical model takes into account the fluid flow dynamics that result in ripple periods shorter than the wavelength of the surface plasmon polaritons. Theoretical and experimental results are reported for incident angles of 0° and 45° relative to the surface normal. There is agreement between the experimentally measured and the theoretically predicted ripple periodicity for 50 pulses at 0° incidence. By contrast, for 100 pulses at 0° incidence, and 50 and 100 pulses at 45° incidence, the experimentally measured ripples have a larger period than the one predicted by the model while the trends in period with increased incident angle, and increased fluence are in agreement between the experimental and the theoretical results.

Nemo: a computational tool for analyzing nematode locomotion.

BACKGROUND: The nematode Caenorhabditis elegans responds to an impressive range of chemical, mechanical and thermal stimuli and is extensively used to investigate the molecular mechanisms that mediate chemosensation, mechanotransduction and thermosensation. The main behavioral output of these responses is manifested as alterations in animal locomotion. Monitoring and examination of such alterations requires tools to capture and quantify features of nematode movement. RESULTS: In this paper, we introduce Nemo (nematode movement), a computationally efficient and robust two-dimensional object tracking algorithm for automated detection and analysis of C. elegans locomotion. This algorithm enables precise measurement and feature extraction of nematode movement components. In addition, we develop a Graphical User Interface designed to facilitate processing and interpretation of movement data. While, in this study, we focus on the simple sinusoidal locomotion of C. elegans, our approach can be readily adapted to handle complicated locomotory behaviour patterns by including additional movement characteristics and parameters subject to quantification. CONCLUSION: Our software tool offers the capacity to extract, analyze and measure nematode locomotion features by processing simple video files. By allowing precise and quantitative assessment of behavioral traits, this tool will assist the genetic dissection and elucidation of the molecular mechanisms underlying specific behavioral responses.

Semi-automated Acanthamoeba polyphaga detection and computation of Salmonella typhimurium concentration in spatio-temporal images.

Interaction between bacteria and protozoa is an increasing area of interest, however there are a few systems that allow extensive observation of the interactions. A semi-automated approach is proposed to analyse a large amount of experimental data and avoid a time demanding manual object classification. We examined a surface system consisting of non nutrient agar with a uniform bacterial lawn that extended over the agar surface, and a spatially localised central population of amoebae. Location and identification of protozoa and quantification of bacteria population are performed by the employment of image analysis techniques in a series of spatial images. The quantitative tools are based on intensity thresholding, or on probabilistic models. To accelerate organism identification, correct classification errors and attain quantitative details of all objects a custom written Graphical User Interfaces has also been developed.

Distinct intracellular motifs of Delta mediate its ubiquitylation and activation by Mindbomb1 and Neuralized.

DSL proteins are transmembrane ligands of the Notch receptor. They associate with a RING (really interesting new gene) family E3 ubiquitin ligase, either Neuralized (Neur) or Mindbomb 1 (Mib1), as a prerequisite to signaling. Although Neur and Mib1 stimulate internalization of DSL ligands, it is not known how ubiquitylation contributes to signaling. We present a molecular dissection of the intracellular domain (ICD) of Drosophila melanogaster Delta (Dl), a prototype DSL protein. Using a cell-based assay, we detected ubiquitylation of Dl by both Neur and Mib1. The two enzymes use distinct docking sites and displayed different acceptor lysine preferences on the Dl ICD. We generated Dl variants that selectively perturb its interactions with Neur or Mib1 and analyzed their signaling activity in two in vivo contexts. We found an excellent correlation between the ability to undergo ubiquitylation and signaling. Therefore, ubiquitylation of the DSL ICD seems to be a necessary step in the activation of Notch.

A complete mathematical study of a 3D model of heterogeneous and anisotropic glioma evolution.

Glioma is the most aggressive type of brain cancer. Several mathematical models have been developed towards identifying the mechanism of tumor growth. The most successful models have used variations of the diffusion-reaction equation, with the recent ones taking into account brain tissue heterogeneity and anisotropy. However, to the best of our knowledge, there hasn't been any work studying in detail the mathematical solution and implementation of the 3D diffusion model, addressing related heterogeneity and anisotropy issues. To this end, this paper introduces a complete mathematical framework on how to derive the solution of the equation using different numerical approximation of finite differences. It indicates how different proliferation rate schemes can be incorporated in this solution and presents a comparative study of different numerical approaches.

Dynamic behavior of GFP-CLIP-170 reveals fast protein turnover on microtubule plus ends.

Microtubule (MT) plus end-tracking proteins (+TIPs) specifically recognize the ends of growing MTs. +TIPs are involved in diverse cellular processes such as cell division, cell migration, and cell polarity. Although +TIP tracking is important for these processes, the mechanisms underlying plus end specificity of mammalian +TIPs are not completely understood. Cytoplasmic linker protein 170 (CLIP-170), the prototype +TIP, was proposed to bind to MT ends with high affinity, possibly by copolymerization with tubulin, and to dissociate seconds later. However, using fluorescence-based approaches, we show that two +TIPs, CLIP-170 and end-binding protein 3 (EB3), turn over rapidly on MT ends. Diffusion of CLIP-170 and EB3 appears to be rate limiting for their binding to MT plus ends. We also report that the ends of growing MTs contain a surplus of sites to which CLIP-170 binds with relatively low affinity. We propose that the observed loss of fluorescent +TIPs at plus ends does not reflect the behavior of single molecules but is a result of overall structural changes of the MT end.