Modelling Competing Endogenous RNA Networks

MicroRNAs (miRNAs) are small RNA molecules, about 22 nucleotide long, which post-transcriptionally regulate their target messenger RNAs (mRNAs). They accomplish key roles in gene regulatory networks, ranging from signaling pathways to tissue morphogenesis, and their aberrant behavior is often associated with the development of various diseases. Recently it has been experimentally shown that the way miRNAs interact with their targets can be described in terms of a titration mechanism. From a theoretical point of view titration mechanisms are characterized by threshold effect at near-equimolarity of the different chemical species, hypersensitivity of the system around the threshold, and cross-talk among targets. The latter characteristic has been lately identified as competing endogenous RNA (ceRNA) effect to mark those indirect interactions among targets of a common pool of miRNAs they are in competition for. Here we propose a stochastic model to analyze the equilibrium and out-of-equilibrium properties of a network of miRNAs interacting with mRNA targets. In particular we are able to describe in detail the peculiar equilibrium and non-equilibrium phenomena that the system displays in proximity to the threshold: (i) maximal cross-talk and correlation between targets, (ii) robustness of ceRNA effect with respect to the model's parameters and in particular to the catalyticity of the miRNA-mRNA interaction, and (iii) anomalous response-time to external perturbations

Nucleation dynamics in 2d cylindrical Ising models and chemotaxis

The aim of our work is to study the effect of geometry variation on nucleation times and to address its role in the context of eukaryotic chemotaxis (i.e. the process which allows cells to identify and follow a gradient of chemical attractant). As a first step in this direction we study the nucleation dynamics of the 2d Ising model defined on a cylindrical lattice whose radius changes as a function of time. Geometry variation is obtained by changing the relative value of the couplings between spins in the compactified (vertical) direction with respect to the horizontal one. This allows us to keep the lattice size unchanged and study in a single simulation the values of the compactification radius which change in time. We show, both with theoretical arguments and numerical simulations that squeezing the geometry allows the system to speed up nucleation times even in presence of a very small energy gap between the stable and the metastable states. We then address the implications of our analysis for directional chemotaxis. The initial steps of chemotaxis can be modelled as a nucleation process occurring on the cell membrane as a consequence of the external chemical gradient (which plays the role of energy gap between the stable and metastable phases). In nature most of the cells modify their geometry by extending quasi-onedimensional protrusions (filopodia) so as to enhance their sensitivity to chemoattractant. Our results show that this geometry variation has indeed the effect of greatly decreasing the timescale of the nucleation process even in presence of very small amounts of chemoattractants.Comment: 27 pages, 6 figures and 2 table

Polarized micro-Raman studies of femtosecond laser written stress-induced optical waveguides in diamond

Understanding the physical mechanisms of the refractive index modulation induced by femtosecond laser writing is crucial for tailoring the properties of the resulting optical waveguides. In this work we apply polarized Raman spectroscopy to study the origin of stress-induced waveguides in diamond, produced by femtosecond laser writing. The change in the refractive index induced by the femtosecond laser in the crystal is derived from the measured stress in the waveguides. The results help to explain the waveguide polarization sensitive guiding mechanism, as well as providing a technique for their optimization.Comment: 5 pages, 4 figure

Creation of pure non-crystalline diamond nanostructures via room-temperature ion irradiation and subsequent thermal annealing

Carbon exhibits a remarkable range of structural forms, due to the availability of sp3, sp2 and sp1 chemical bonds. Contrarily to other group IV elements such as silicon and germanium, the formation of an amorphous phase based exclusively on sp3 bonds is extremely challenging due to the strongly favored formation of graphitic-like structures at room 19 temperature and pressure. As such, the formation of a fully sp3-bonded carbon phase requires 20 an extremely careful (and largely unexplored) definition of the pressure and temperature across the phase diagram. Here, we report on the possibility of creating full-sp3 amorphous nanostructures within the bulk crystal of diamond with room-temperature ion-beam irradiation, followed by an annealing process that does not involve the application of any external mechanical pressure. As confirmed by numerical simulations, the (previously unreported) radiation-damage-induced formation of an amorphous sp2-free phase in diamond is determined by the buildup of extremely high internal stresses from the surrounding lattice, which (in the case of nanometer-scale regions) fully prevent the graphitization process. Besides the relevance of understanding the formation of exotic carbon phases, the use of focused/collimated ion beams discloses appealing perspectives for the direct fabrication of such nanostructures in complex three-dimensional geometries

Micro-beam and pulsed laser beam techniques for the micro-fabrication of diamond surface and bulk structures

Micro-fabrication in diamond is involved in a wide set of emerging technologies, exploiting the exceptional characteristics of diamond for application in bio-physics, photonics, radiation detection. Micro ion-beam irradiation and pulsed laser irradiation are complementary techniques, which permit the implementation of complex geometries, by modification and functionalization of surface and/or bulk material, modifying the optical, electrical and mechanical characteristics of the material. In this article we summarize the work done in Florence (Italy) concerning ion beam and pulsed laser beam micro-fabrication in diamond.Comment: 14 pages, 5 figure

Proof of concept of a frequency-preserving and time-invariant metamaterial-based nonlinear acoustic diode

Acoustic filters and metamaterials have become essential components for elastic wave control in applications ranging from ultrasonics to noise abatement. Other devices have been designed in this field, emulating their electromagnetic counterparts. One such case is an acoustic diode or rectifier, which enables one-way wave transmission by breaking the wave equation-related reciprocity. Its achievement, however, has proved to be rather problematic, and current realizations display a number of shortcomings in terms of simplicity and versatility. Here, we present the design, fabrication and characterization of a device able to work as an acoustic diode, a switch and a transistor-like apparatus, exploiting symmetry-breaking nonlinear effects like harmonic generation and wave mixing, and the filtering capabilities of metamaterials. This device presents several advantages compared with previous acoustic diode realizations, including versatility, time invariance, frequency preserving characteristics and switchability. We numerically evaluate its efficiency and demonstrate its feasibility in a preliminary experimental realization. This work may provide new opportunities for the practical realization of structural components with one-way wave propagation properties

Bio-inspired non self-similar hierarchical elastic metamaterials

Hierarchy provides unique opportunities for the design of advanced materials with superior properties that arise from architecture, rather than from constitutive material response. Contrary to the quasi-static regime, where the potential of hierarchy has been largely explored, its role in vibration mitigation and wave manipulation remains elusive. So far, the majority of the studies concerning hierarchical elastic metamaterials have proposed a selfsimilar repetition of a specific unit cell at multiple scale levels, leading to the activation of the same bandgap mechanism at different frequencies. On the contrary, here, we show that by designing non self-similar hierarchical geometries allows us to create periodic structures supporting multiple, highly attenuative and broadband bandgaps involving (independently or simultaneously) different scattering mechanisms, namely, Bragg scattering, local resonance and/or inertial amplification, at different frequencies. The type of band gap mechanism is identified and discussed by examining the vibrational mode shapes and the imaginary component of the wavenumber in the dispersion diagram of the unit cell. We also experimentally confirm this by performing measurements in the lowest frequency regime on a 3D printed structure. Hierarchical design strategies may find application in vibration mitigation for civil, aerospace and mechanical engineering

Hierarchical auxetic and isotropic porous medium with extremely negative Poisson's ratio

We propose a novel two-dimensional hierarchical auxetic structure consisting of a porous medium in which a homogeneous matrix includes a rank-two set of cuts characterised by different scales. The six-fold symmetry of the perforations makes the medium isotropic in the plane. Remarkably, the mesoscale interaction between the first- and second-level cuts enables the attainment of a value of the Poisson's ratio close to the minimum reachable limit of -1. The effective properties of the hierarchical auxetic structure are determined numerically, considering both a unit cell with periodic boundary conditions and a finite structure containing a large number of repeating cells. Further, results of the numerical study are validated experimentally on a polymeric specimen with appropriately arranged rank-two cuts, tested under uniaxial tension. We envisage that the proposed hierarchical design can be useful in numerous engineering applications exploiting an extreme auxetic effect

Large scale mechanical metamaterials as seismic shields

MM acknowledges funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 658483. AK acknowledges funding from the European Union's Seventh Framework programme for research and innovation under the Marie Skłodowska-Curie grant agreement no. 609402-2020 researchers: Train to Move (T2M). NMP is supported by the European Research Council (ERC StG Ideas 2011 BIHSNAM no. 279985 and ERC PoC 2015 SILKENE no. 693670), and by the European Commission under the Graphene Flagship (WP 14 Polymer Nanocomposites, no. 696656). FB is supported by BIHSNAM