Edoardo De Tommasi

Optical properties of diatom nanostructured biosilica in Arachnoidiscus sp: micro-optics from mother nature.

Some natural structures show three-dimensional morphologies on the micro- and nano- scale, characterized by levels of symmetry and complexity well far beyond those fabricated by best technologies available. This is the case of diatoms, unicellular microalgae, whose protoplasm is enclosed in a nanoporous microshell, made of hydrogenated amorphous silica, called frustule. We have studied the optical properties of Arachnoidiscus sp. single valves both in visible and ultraviolet range. We found photonic effects due to diffraction by ordered pattern of pores and slits, accordingly to an elaborated theoretical model. For the first time, we experimentally revealed spatial separation of focused light in different spots, which could be the basis of a micro-bio-spectrometer. Characterization of such intricate structures can be of great inspiration for photonic devices of next generation.

Fabrication and characterization of a porous silicon based microarray for label-free optical monitoring of biomolecular interactions

We have fabricated a microarray of porous silicon Bragg reflectors on a crystalline silicon substrate using a technological process based on standard photolithography and electrochemical anodization of the silicon. The array density is of 170 elements/cm2 and each element has a diameter of 200 μm. The porous silicon structures have been used as platform to immobilize an amino terminated DNA single strand probe. All fabrication steps have been monitored by spectroscopic reflectometry, optical and electron microscopy, and Fourier transform infrared spectroscopy. A label-free detection method has been employed to investigate the hybridization between micromolar DNA probe and its complementary target. Due to fast and low cost production, good reproducibility, and high quality optical features, this platform could be adopted also for other different microarray applications such as proteomics and medical diagnostics.

Porous Silicon Based Resonant Mirrors for Biochemical Sensing

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 label-free optical biosensor.

Shedding light on diatom photonics by means of digital holography

Diatoms are among the dominant phytoplankters in the worlds oceans, and their external silica investments, resembling artificial photonic crystals, are expected to play an active role in light manipulation. Digital holography allowed studying the interaction with light of Coscinodiscus wailesii cell wall reconstructing the light confinement inside the cell cytoplasm, condition that is hardly accessible via standard microscopy. The full characterization of the propagated beam, in terms of quantitative phase and intensity, removed a long-standing ambiguity about the origin of the light confinement. The data were discussed in the light of living cell behavior in response to their environment.

Plasmon-like surface states in negative refractive index photonic crystals

In this paper, the presence of localized plasmon-like modes at the surface of a silicon two-dimensional photonic crystal slab is demonstrated. In analogy with surface plasmons supported in metals, we observe that, in a photonic crystal metamaterial, the electromagnetic surface waves arise from a negative effective permittivity. The proposed device is dimensioned in order to support surface states in a large spectral window (≃1550–1650 nm). The result opens strategies in light control at the nanoscale, allowing on chip light manipulation in a wide frequency range and avoiding the intrinsic limits of plasmonic structures due to absorption losses in metals.

Label-free biosensing by means of optical micro-ring resonator

Micro-ring resonators have been widely employed, in recent years, as wavelength filters, switches and frequency converters in optical communication circuits, but can also be successfully used as transducing elements in optical sensing and biosensing. Their operation is based on the optical coupling between a ring-shaped waveguide and one or more linear waveguides patterned on a planar surface, typically an input and an output waveguide. When incoming light has a wavelength which satisfies the resonance conditions, it couples into the micro-ring and continuously re-circulates within it. A fraction of this resonant light escapes the micro-ring structure and couples into the output waveguide. The presence of a target analyte over the top surface of the micro-ring (i.e. within the evanescent field) changes the effective refractive index of the mode propagating into the structure, thus causing a shift in resonance wavelength which can be determined by monitoring the spectrum at the output port. Proper functionalization of the micro-ring surface allows to add selectivity to the sensing system and to detect specific interaction between a bioprobe and its proper target (e.g. protein-ligand, DNA-cDNA interactions). We present our preliminary results on the design of micro-ring resonators on silicon-on-insulator substrate, aimed at selective detection of several biomolecules. The design of the structure has been accomplished with the help of FDTD 2D numerical simulations of the distribution of the electromagnetic fields inside the waveguides, the micro-ring and near the micro-ring surface. Furthermore, all the functionalization reactions and the bio/non-bio interfaces have been studied and modelled by means of spectroscopic ellipsometry.

Bioderived Three-Dimensional Hierarchical Nanostructures as Efficient Surface-Enhanced Raman Scattering Substrates for Cell Membrane Probing

In this work, we propose the use of complex, bioderived nanostructures as efficient surface-enhanced Raman scattering (SERS) substrates for chemical analysis of cellular membranes. These structures were directly obtained from a suitable gold metalization of the Pseudonitzchia multistriata diatom silica shell (the so called frustule), whose grating-like geometry provides large light coupling with external radiation, whereas its extruded, subwavelength lateral edge provides an excellent interaction with cells without steric hindrance. We carried out numerical simulations and experimental characterizations of the supported plasmonic resonances and optical near-field amplification. We thoroughly evaluated the SERS substrate enhancement factor as a function of the metalization parameters and finally applied the nanostrucures for discriminating cell membrane Raman signals. In particular, we considered two cases where the membrane composition plays a fundamental role in the assessment of several pathologies, that is, red blood cells and B-leukemia REH cells.

Diatom Valve Three-Dimensional Representation: A New Imaging Method Based on Combined Microscopies

The frustule of diatoms, unicellular microalgae, shows very interesting photonic features, generally related to its complicated and quasi-periodic micro- and nano-structure. In order to simulate light propagation inside and through this natural structure, it is important to develop three-dimensional (3D) models for synthetic replica with high spatial resolution. In this paper, we present a new method that generates images of microscopic diatoms with high definition, by merging scanning electron microscopy and digital holography microscopy or atomic force microscopy data. Starting from two digital images, both acquired separately with standard characterization procedures, a high spatial resolution (Δz = λ/20, Δx = Δy ≅ 100 nm, at least) 3D model of the object has been generated. Then, the two sets of data have been processed by matrix formalism, using an original mathematical algorithm implemented on a commercially available software. The developed methodology could be also of broad interest in the design and fabrication of micro-opto-electro-mechanical systems.

Integrated optical biosensors and biochips based on porous silicon technology

Micro-total-analysis-systems and lab-on-chip are more than promises in lot of social interest applications such as clinical diagnostic or environmental monitoring. There is an increasing demand of new and customized devices with better performances to be used in very specific applications. Nanostructured Porous silicon is a functional material and a versatile platform for the fabrication of integrated optical microsystems to be used in biochemical analysis. Our research activity is focused on the design, the fabrication and the characterization of several photonic porous silicon based structures, which are used in the sensing of specific molecular interactions. To integrate the porous silicon based optical transducer in biochip devices we have modified standard micromachining processes, such as anodic bonding and photo-patterning, in order to make them consistent to the utilization of biological probes.

Optical sensing of chemicals by a porous silicon Bragg grating waveguide

A direct laser writing process has been exploited to fabricate a high order Bragg grating on the surface of a porous silicon slab waveguide. The transmission spectrum of the structure, characterized by a pitch of 10 µm, has been investigated by end-fire coupling on exposure to vapor substances of environmental interest. The analyte molecules substitute the air into the silicon pores, due to the capillary condensation phenomenon, and the transmitted spectrum of the grating shifts towards higher wavelengths. The experimental results have been compared with the theoretical calculations obtained by using the transfer matrix method together with the slab waveguide modal calculation.