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Hydrophobins are small proteins secreted by fungi, which self-assemble into amphipathic membranes at air-liquid or liquid-solid interfaces. The physical and chemical properties of some hydrophobins, both in solution and as a biofilm, are affected by poly or oligosaccharides. We have studied the interaction between glucose and the hydrophobin Vmh2 from Pleurotus ostreatus by spectroscopic ellipsometry (SE), atomic force microscopy (AFM) and water contact angle (WCA). We have found that Vmh2-glucose complexes forms a chemically stable biofilm, obtained by drop deposition on silicon, 1.6 nm thick and containing 35 per cent of glucose, quantified by SE. AFM highlighted the presence of nanometric rodlet-like aggregates (average height, width and length being equal to 3.6, 23.8 and 40 nm, respectively) on the biofilm surface, slightly different from those obtained in the absence of glucose (4.11, 23.9 and 64 nm). The wettability of a silicon surface, covered by the organic layer of Vmh2-glucose, strongly changed: WCA decreased from 90° down to 17°.

In this paper, design, fabrication and characterization of an all-silicon photodetector (PD) at 1550 nm, have been reported. Our device is a surface-illuminated PD constituted by a Fabry-Perot microcavity incorporating a Cu/p-Si Schottky diode. Its absorption mechanism, based on the internal photoemission effect (IPE), has been enhanced by critical coupling condition. Our experimental findings prove a peak responsivity of 0.063 mA/W, which is the highest value obtained in a surface-illuminated IPE-based Si PD around 1550 nm. Finally, device capacitance measurements have been carried out demonstrating a capacitance < 5 pF which has the potential for GHz operation subject to a reduction of the series resistance of the ohmic contact.

A porous silicon (PSi) based microarray has been integrated with a microfluidic system, as a proof of concept device for the optical monitoring of selective label-free DNA-DNA interaction. A 4 × 4 square matrix of PSi one dimensional photonic crystals, each one of 200 μm diameter and spaced by 600 μm, has been sealed by a polydimethylsiloxane (PDMS) channels circuit. The PSi optical microarray elements have been functionalized by DNA single strands after sealing: the microfluidic circuit allows to reduce significantly the biologicals and chemicals consumption, and also the incubation time with respect to a not integrated device. Theoretical calculations, based on finite element method, taking into account molecular interactions, are in good agreement with the experimental results, and the developed numerical model can be used for device optimization. The functionalization process and the interaction between DNA probe and target has been monitored by spectroscopic reflectometry for each PSi element in the microchannels.

Finite element method analysis was applied to the characterization of the biomolecular interactions taking place in a microfluidic assisted microarray. Numerical simulations have been used for the optimization of geometrical and physical parameters of the sensing device. Different configurations have been analyzed and general considerations have been derived. We have shown that a parallel disposition of the sensing area allows the homogeneous formation of the target molecular complex in all the active zones of the microarray. Stationary and time dependent results have also been obtained.

In this paper we discuss and experimentally demonstrate that in a quasi- zero-average-refractive-index (QZAI) metamaterial, in correspondence of a divergent source in near infrared (λ = 1.55 μm) the light scattered out is extremely directive (Δθ(out) = 0.06°), coupling with diffraction order of the alternating complementary media grating. With a high degree of accuracy the measurements prove also the excellent vertical confinement of the beam even in the air region of the metamaterial, in absence of any simple vertical confinement mechanism. This extremely sensitive device works on a large contact area and open news perspective to integrated spectroscopy.

Due to recent breakthroughs, silicon photonics is now the most active discipline within the field of integrated optics and, at the same time, a present reality with commercial products available on the market. Silicon photodiodes are excellent detectors at visible wavelengths, but the development of high-performance photodetectors on silicon CMOS platforms at wavelengths of interest for telecommunications has remained an imperative but unaccomplished task so far. In recent years, however, a number of near-infrared all-silicon photodetectors have been proposed and demonstrated for optical interconnect and power-monitoring applications. In this paper, a review of the state of the art is presented. Devices based on mid-bandgap absorption, surface-state absorption, internal photoemission absorption and two-photon absorption are reported, their working principles elucidated and their performance discussed and compared.

The protein-ligand molecular interactions imply strong geometrical and structural rearrangements of the biological complex which are normally detected by high sensitivity optical techniques such as time-resolved fluorescence microscopy. In this work, we have measured, by optical spectroscopic reflectometry in the visible-near-infrared region, the interaction between a sugar binding protein (SBP), covalently bound on the surface of a porous silicon (PSi) microcavity, and glucose, at different concentrations and temperatures. Variable-angle spectroscopic ellipsometric (VASE) characterization of protein-functionalized PSi layers confirms that the protein-ligand system has an overall volume smaller than the SBP alone.

We report on our preliminary results in the realization and characterization of a porous silicon (PSi) resonant mirror (RM) for optical biosensing. We have numerically and experimentally studied the coupling between the electromagnetic field, totally reflected at the base of a high refractive index prism, and the optical modes of a PSi waveguide. This configuration is very sensitive to changes in the refractive index and/or in thickness of the sensor surface. Due to the high specific area of the PSi waveguide, very low DNA concentrations can be detected confirming that the RM could be a very sensitive and labelfree optical biosensor.

We have investigated the laser induced ablation-oxidation process on porous silicon layers having different porosities and thicknesses by non-destructive optical techniques. In particular, the interaction between a low power blue light laser and the porous silicon surfaces has been characterized by variable angle spectroscopic ellipsometry and Fourier transform infrared spectroscopy. The oxidation profiles etched on the porous samples can be tuned as functions of the layer porosity and laser fluence. Oxide stripes of width less than 2 µm and with thicknesses between 100 nm and 5 µm have been produced, depending on the porosity of the porous silicon, by using a 40 × focusing objective.

The D-trehalose/D-maltose-binding protein (TMBP), a monomeric protein of 48 kDa, is one component of the trehalose and maltose (Mal) uptake system. In the hyperthermophilic archaeon Thermococcus litoralis, this is mediated by a protein-dependent ATP-binding cassette system transporter. The gene coding for a thermostable TMBP from the archaeon T. litoralis has been cloned, and the recombinant protein has been expressed in E. coli. The recombinant TMBP has been purified to homogeneity and characterized. It exhibits the same functional and structural properties as the native one. In fact, it is highly thermostable and binds sugars, such as maltose, trehalose and glucose, with high affinity. In this work, we have immobilized TMBP on a porous silicon wafer. The immobilization of TMBP to the chip was monitored by reflectivity and Fourier Transformed Infrared spectroscopy. Furthermore, we have tested the optical response of the protein-Chip complex to glucose binding. The obtained data suggest the use of this protein for the design of advanced optical non-consuming analyte biosensors for glucose detection.

In this work, we report on the light focusing ability exploited by the microshell of a marine organism: the Coscinodiscus wailesii diatom. A 100 microm spot size of a red laser beam is narrowed up to less than 10 microm at a distance of 104 microm after the transmission through the regular geometry of the diatom structure, which thus acts as a microlens. Numerical simulations of the electromagnetic field propagation show a good qualitative agreement with the experimental results. The focusing effect is due to the superposition of the waves scattered by the holes present on the surface of the diatom valve. Very interesting applications in micro-optic devices are feasible due to the morphological and biological characteristic of these unicellular organisms.

The anisotropic wet micromachining of silicon, based on a water solution of potassium hydroxide (KOH), is a standard fabrication process that is extensively exploited in the realization of very complex microsystems, which comprise cantilevers, membranes, and bridges. A nanostructured self-assembled biofilm of amphiphilic proteins, the hydrophobins, was deposited on crystalline silicon by solution deposition and characterized by variable-angle spectroscopic ellipsometry (VASE). This procedure formed chemically and mechanically stable mono- and multilayers of self-assembled proteins. The biomolecular membrane has been tested as masking material in the KOH wet etch of the crystalline silicon. The process has been monitored by VASE and atomic force microscopy measurements. Because of the high persistence of the protein biofilm, the hydrophobin-coated silicon surface is perfectly protected during the standard KOH micromachining process.

When a wave impinges obliquely to the interface of a Photonic Crystal (PhC), the wave can be completely reflected in counter-propagating direction instead of the usually expected specular direction. However the beam is totally specularly reflected with a simple modification of the surface termination. The analysis of the time average Poynting vector evidences that PhC termination modifies the energy flow and determines the reflection properties.

Dielectric aperiodic Thue-Morse structures up to 128 layers have been fabricated by using porous silicon technology. The photonic band gap properties of Thue-Morse multilayers have been theoretically investigated by means of the transfer matrix method and the integrated density of states. The theoretical approach has been compared and discussed with the reflectivity measurements at variable angles for both the transverse electric and transverse magnetic polarizations of light. The photonic band gap regions, wide 70 nm and 90 nm, included between 0 and 30 degrees , have been observed for the sixth and seventh orders, respectively.

In this work, the binding of the recombinant glutamine-binding protein (GlnBP) from Escherichia coli to gliadin peptides, toxic for celiac patients, was investigated by mass spectrometry experiments and optical techniques. Mass spectrometry experiments demonstrated that GlnBP binds the following amino acid sequence: XXQPQPQQQQQQQQQQQQL, present only into the toxic prolamines. The binding of GlnBP to gliadin suggested us to design a new optical biosensor based on nanostructured porous silicon (PSi) for the detection of trace amounts of gliadin in food. The GlnBP, which acts as a molecular probe for the gliadin, was covalently linked to the surface of the PSi wafer by a proper passivation process. The GlnBP-gliadin interaction was revealed as a shift in wavelength of the fringes in the reflectivity spectrum of the PSi layer. The GlnBP, covalently bonded to the PSi chip, selectively recognized the toxic peptide. Finally, the sensor response to the protein concentration was measured in the range 2.0-40.0 microg/L and the sensitivity of the sensor was determined.

The molecular binding between the glutamine-binding protein (GlnBP) from Escherichia coli and L-glutamine (Gln) is optically transduced by means of a biosensor based on porous silicon nano-technology. The sensor operates by the measurement of the interferometric fringes in the reflectivity spectrum of a porous silicon Fabry-Perot layer. The binding event is revealed as a shift in wavelength of the fringes. Due to the hydrophobic interaction with the Si-H terminated surface of the porous silicon, the GlnBP protein, which acts as a molecular probe for Gln, penetrates and links into the pores of the porous silicon matrix. We can thus avoid any preliminary functionalization process of the porous layer surface, which is also prevented from oxidation, at least for few cycles of wet measurements. The binding of Gln to GlnBP has also been investigated at different concentration of GlnBP.

A simple and low cost optical sensor, based on porous silicon nanotechnology, has been used to detect and quantify the presence of atrazine pesticide in water and humic acid solutions. In both cases, a well defined optical signal variation can be registered, even at low concentration as 1 ppm. The phenomenon can be ascribed to the capillary infiltration of liquid into the pores, which changes the average refractive index of the structure. Due to the resonant cavity enhanced operation of the proposed sensors, very low detection limits can be reached.

A simple geometry optical sensor based on porous silicon technology is theoretically and experimentally studied. We expose some porous silicon optical microcavities with different porous structures to several substances of environmental interest: Very large red shifts in the single transmission peak in the reflectivity spectrum due to changes in the average refractive index are observed. The phenomenon can be ascribed to capillary condensation of vapor phases in the silicon pores. We numerically compute the peak shifts as a function of the liquid volume fraction condensed into the stack by using the Bruggeman theory. The results presented are promising for vapor and liquid detection and identification.

Rendina et al. recently proposed the original configuration of an electromagnetic power sensor for microwaves and millimeter waves that is based on an optically interrogated all-silicon chip [Electron. Lett. 35, 1748 (1999)]. Here we theoretically analyze and discuss in detail the performances of such a new class of nonperturbing and wideband probe in terms of sensitivity, resolution, intrinsic detectivity, linearity, and response time. Good agreement between theory and experiments is demonstrated. In particular, minimum resolutions of approximately 1 mW/cm2 are obtained at frequencies beyond 10 GHz. The dependence of response on the geometrical and electromagnetic parameters of the sensing element is analyzed, and on this basis the possibility of achieving optimized configurations is discussed.

The operation at 1.5 microm of a silicon Fabry-Perot optical modulator is reported. The electrically driven device, which uses the thermo-optic effect to achieve as much as a 55% intensity modulation depth, has been realized by means of standard silicon microelectronic technology. This demonstrates that this new type of optical modulator can easily be integrated with electronic circuits. An accurate three-dimensional thermal analysis of the device has permitted the setup of a reliable numerical code aimed at the design of optimized integrated versions of it. The simulation outputs therefore predict operation frequencies of hundreds of kilohertz, remarkably superior to those previously reported in thermo-optic-effect-based modulators.

A detailed analysis of tapered and inhomogeneous dielectric light collectors was worked out for both illumination and solar energy applications. In particular, tapered dielectric guides have been investigated both theoretically and experimentally together with their capability to collect and transmit high fluxes of light energy. Furthermore, GRIN rods are considered as matching devices, to improve the collecting performance of tapered guides.