EGAC: a genetic algorithm to compare chemical reaction networks

Discovering relations between chemical reaction networks (CRNs) is a relevant problem in computational systems biology for model reduction, to explain if a given system can be seen as an abstraction of another one; and for model comparison, useful to establish an evolutionary path from simpler networks to more complex ones. This is also related to foundational issues in computer science regarding program equivalence, in light of the established interpretation of a CRN as a kernel programming language for concurrency. Criteria for deciding if two CRNs can be formally related have been recently developed, but these require that a candidate mapping be provided. Automatically finding candidate mappings is very hard in general since the search space essentially consists of all possible partitions of a set. In this paper we tackle this problem by developing a genetic algorithm for a class of CRNs called influence networks, which can be used to model a variety of biological systems including cell-cycle switches and gene networks. An extensive numerical evaluation shows that our approach can successfully establish relations between influence networks from the literature which cannot be found by exact algorithms due to their large computational requirements

Near to short wave infrared light generation through AlGaAs-on-insulator nanoantennas

AlGaAs-on-insulator (AlGaAs-OI) has recently emerged as a novel promising platform for nonlinear optics at the nanoscale. Among the most remarkable outcomes, second harmonic generation (SHG) in the visible/near infrared spectral region has been demonstrated in AlGaAs-OI nanoantennas (NA). In order to extend the nonlinear frequency generation towards the short wave infrared window, in this work we propose and demonstrate via numerical simulations difference frequency generation (DFG) in AlGaAs-OI NAs. The NA geometry is finely adjusted in order to obtain simultaneous optical resonances at the pump, signal and idler wavelengths, which results in an efficient DFG with conversion efficiencies up to 0.01%. Our investigation includes the study of the robustness against random variations of the NA geometry that may occur at fabrication stage. Overall, these outcomes identify a new potential and yet unexplored application of AlGaAs-OI NAs as compact devices for the generation and control of the radiation pattern in the near to short infrared spectral region

High-aspect-ratio dielectric pillar with nanocavity backed by metal substrate in the infrared range

We investigated absorption and field enhancements of shallow nanocavities on top of high-aspect-ratio dielectric pillars in the infrared range. The structure includes a high-aspect-ratio nanopillar array of high refractive index, with nano-cavities on top of the pillars, and a metal plane at the bottom. The enhancement factor of electric field intensity reaches 3180 in the nanocavities and peak absorption reaches 99% . We also investigated the finite-size effect of the presented structure to simulate real experiments. Due to its narrow absorption bandwidth 3.5 nm, it can work as a refractive index sensor with sensitivity 297.5 nm/RIU and figure of merit 85. This paves the way to directly control light field at the nanoscales in the infrared light range. The investigated nanostructure will find applications in multifunctional photonics devices such as chips for culturing cells, refractive index sensors, biosensors of single molecule detection and nonlinear sensors

Second order nonlinear optics in AlGaAs metasurfaces

Recently, nonlinear optics at the nanoscale level has emerged as a promising branch of nanophotonics. In this work, we focus our attention on Aluminum Gallium Arsenide (AlGaAs) nanoantennas and metasurfaces for efficient and controlled second harmonic photon emission. After a brief introduction concerning the main studies in this field, we present the latest results achieved in AlGaAs platforms both in the lossless and absorption regimes

Enhancing second harmonic generation by Q-boosting lossless cavities beyond the time bandwidth limit

Nanostructures proved to be versatile platforms to control the electromagnetic field at subwavelength scale. Indeed, high-quality-factors nanocavities have been used to boost and control nonlinear frequency generation by increasing the light-matter interaction. However, nonlinear processes are triggered by high-intensities, which are provided by ultrashort laser pulses with large bandwidth, that cannot be fully exploited in such devices. Time-varying optical systems allow one to overcome the time-bandwidth limit by modulating the cavity external coupling. Here we present a general treatment, based on coupled mode theory, to describe second harmonic generation in a doubly resonant cavity for which the quality-factor at the fundamental frequency is modulated in time. We identify the initial quality factor maximizing second harmonic efficiency when performing Q-boosting and we predict a theoretical conversion efficiency close to unity. Our results have direct impact on the design of next generation time-dependent metasurfaces to boost nonlinear frequency conversion of ultrashort laser pulses

Manipulating Light with Tunable Nanoantennas and Metasurfaces

The extensive progress in nanofabrication techniques enabled innovative methods for molding light at the nanoscale. Subwavelength structured optical elements and, in general, metasurfaces and metamaterials achieved promising results in several research areas, such as holography, microscopy, sensing and nonlinear optics. Still, a demanding challenge is represented by the development of innovative devices with reconfigurable optical properties. Here, we review recent achievements in the field of tunable metasurface. After a brief general introduction about metasurfaces, we will discuss two different mechanisms to implement tunable properties of optical elements at the nanoscale. In particular, we will first focus on phase-transition materials, such as vanadium dioxide, to tune and control the resonances of dipole nanoantennas in the near-infrared region. Finally, we will present a platform based on an AlGaAs metasurface embedded in a liquid crystal matrix that allows the modulation of the generated second harmonic signal

Opto-thermal dynamics of thin-film optical limiters based on the VO2 phase transition

Protection of human eyes or sensitive detectors from high-intensity laser radiation is an important challenge in modern light technologies. Metasurfaces have proved to be valuable tools for such light control, but the actual possibility of merging multiple materials in the nanofabrication process hinders their application. Here we propose and numerically investigate the opto-thermal properties of plane multilayered structures with phase-change materials for optical limiters. Our structure relies on thin-film VO2 phase change material on top of a gold film and a sapphire substrate. We show how such a multi-layer structure can act as a self-activating device that exploits light-to-heat conversion to induce a phase change in the VO2 layer. We implement a numerical model to describe the temporal evolution of the temperature and transmittivity across the device under both a continuous wave and pulsed illumination. Our results open new opportunities for multi-layer self-activating optical limiters and may be extended to devices based on other phase change materials or different spectral regions

Giant photoinduced reflectivity modulation of nonlocal resonances in silicon metasurfaces

Metasurfaces offer a unique playground to tailor the electromagnetic field at subwavelength scale to control polarization, wavefront, and nonlinear processes. Tunability of the optical response of these structures is challenging due to the nanoscale size of their constitutive elements. A long-sought solution to achieve tunability at the nanoscale is all-optical modulation by exploiting the ultrafast nonlinear response of materials. However, the nonlinear response of materials is inherently very weak, and, therefore, requires optical excitations with large values of fluence. We show that by properly tuning the equilibrium optical response of a nonlocal metasurface, it is possible to achieve sizable variation of the photoinduced out-of-equilibrium optical response on the picosecond timescale employing fluences smaller than 250 μJ / cm2, which is 1 order of magnitude lower than previous studies with comparable reflectivity variations in silicon platforms. Our results pave the way to fast devices with large modulation amplitude.<br/

Manipulating Light with Tunable Nanoantennas and Metasurfaces

The extensive progress in nanofabrication techniques enabled innovative methods for molding light at the nanoscale. Subwavelength structured optical elements and, in general, metasurfaces and metamaterials achieved promising results in several research areas, such as holography, microscopy, sensing and nonlinear optics. Still, a demanding challenge is represented by the development of innovative devices with reconfigurable optical properties. Here, we review recent achievements in the field of tunable metasurface. After a brief general introduction about metasurfaces, we will discuss two different mechanisms to implement tunable properties of optical elements at the nanoscale. In particular, we will first focus on phase-transition materials, such as vanadium dioxide, to tune and control the resonances of dipole nanoantennas in the near-infrared region. Finally, we will present a platform based on an AlGaAs metasurface embedded in a liquid crystal matrix that allows the modulation of the generated second harmonic signal