A model eye for fluorescent characterization of retinal cultures and tissues.

Many human neural or neurodegenerative diseases strongly affect the ocular and retinal environment showing peculiar alterations which can be employed as specific disease biomarkers. The noninvasive optical accessibility of the retina makes the ocular investigation a potentially competitive strategy for screening, thus the development of retinal biomarkers is rapidly growing. Nevertheless, a tool to study and image biomarkers or biological samples in a human-like eye environment is still missing. Here we report on a modular and versatile eye model designed to host biological samples, such as retinal cultures differentiated from human induced pluripotent stem cells and ex-vivo retinal tissue, but also suited to host any kind of retinal biomarkers. We characterized the imaging performance of this eye model on standard biomarkers such as Alexa Fluor 532 and Alexa Fluor 594.

Optical computation of a spin glass dynamics with tunable complexity.

Spin glasses (SGs) are paradigmatic models for physical, computer science, biological, and social systems. The problem of studying the dynamics for SG models is nondetermistic polynomial-time (NP) hard; that is, no algorithm solves it in polynomial time. Here we implement the optical simulation of an SG, exploiting the N segments of a wavefront-shaping device to play the role of the spin variables, combining the interference downstream of a scattering material to implement the random couplings between the spins (the [Formula: see text] matrix) and measuring the light intensity on a number P of targets to retrieve the energy of the system. By implementing a plain Metropolis algorithm, we are able to simulate the spin model dynamics, while the degree of complexity of the potential energy landscape and the region of phase diagram explored are user defined, acting on the ratio [Formula: see text] We study experimentally, numerically, and analytically this Hopfield-like system displaying a paramagnetic, ferromagnetic, and SG phase, and we demonstrate that the transition temperature [Formula: see text] to the glassy phase from the paramagnetic phase grows with α. We demonstrate the computational advantage of the optical SG where interaction terms are realized simultaneously when the independent light rays interfere on the detector's surface. This inherently parallel measurement of the energy provides a speedup with respect to purely in silico simulations scaling with N.

Behavior of Supercritical Fluids across the "Frenkel Line".

The "Frenkel line" (FL), the thermodynamic locus where the time for a particle to move by its size equals the shortest transverse oscillation period, has been proposed as a boundary between recently discovered liquid-like and gas-like regions in supercritical fluids. We report a simulation study of isothermal supercritical neon in a range of densities intersecting the FL. Specifically, structural properties and single-particle and collective dynamics are scrutinized to unveil the onset of any anomalous behavior at the FL. We find that (i) the pair distribution function smoothly evolves across the FL displaying medium-range order, (ii) low-frequency transverse excitations are observed below the "Frenkel frequency", and (iii) the high-frequency shear modulus does not vanish even for low-density fluids, indicating that positive sound dispersion characterizing the liquid-like region of the supercritical state is unrelated to transverse dynamics. These facts critically undermine the definition of the FL and its significance for any relevant partition of the supercritical phase.

Diffraction-free light droplets for axially-resolved volume imaging.

An ideal direct imaging system entails a method to illuminate on command a single diffraction-limited region in a generally thick and turbid volume. The best approximation to this is the use of large-aperture lenses that focus light into a spot. This strategy fails for regions that are embedded deep into the sample, where diffraction and scattering prevail. Airy beams and Bessel beams are solutions of the Helmholtz Equation that are both non-diffracting and self-healing, features that make them naturally able to outdo the effects of distance into the volume but intrinsically do not allow resolution along the propagation axis. Here, we demonstrate diffraction-free self-healing three-dimensional monochromatic light spots able to penetrate deep into the volume of a sample, resist against deflection in turbid environments, and offer axial resolution comparable to that of Gaussian beams. The fields, formed from coherent mixtures of Bessel beams, manifest a more than ten-fold increase in their undistorted penetration, even in turbid milk solutions, compared to diffraction-limited beams. In a fluorescence imaging scheme, we find a ten-fold increase in image contrast compared to diffraction-limited illuminations, and a constant axial resolution even after four Rayleigh lengths. Results pave the way to new opportunities in three-dimensional microscopy.

Pressure-induced emergence of unusually high-frequency transverse excitations in a liquid alkali metal: Evidence of two types of collective excitations contributing to the transverse dynamics at high pressures.

Unlike phonons in crystals, the collective excitations in liquids cannot be treated as propagation of harmonic displacements of atoms around stable local energy minima. The viscoelasticity of liquids, reflected in transition from the adiabatic to elastic high-frequency speed of sound and in absence of the long-wavelength transverse excitations, results in dispersions of longitudinal (L) and transverse (T) collective excitations essentially different from the typical phonon ones. Practically, nothing is known about the effect of high pressure on the dispersion of collective excitations in liquids, which causes strong changes in liquid structure. Here dispersions of L and T collective excitations in liquid Li in the range of pressures up to 186 GPa were studied by ab initio simulations. Two methodologies for dispersion calculations were used: direct estimation from the peak positions of the L/T current spectral functions and simulation-based calculations of wavenumber-dependent collective eigenmodes. It is found that at ambient pressure, the longitudinal and transverse dynamics are well separated, while at high pressures, the transverse current spectral functions, density of vibrational states, and dispersions of collective excitations yield evidence of two types of propagating modes that contribute strongly to transverse dynamics. Emergence of the unusually high-frequency transverse modes gives evidence of the breakdown of a regular viscoelastic theory of transverse dynamics, which is based on coupling of a single transverse propagating mode with shear relaxation. The explanation of the observed high-frequency shift above the viscoelastic value is given by the presence of another branch of collective excitations. With the pressure increasing, coupling between the two types of collective excitations is rationalized within a proposed extended viscoelastic model of transverse dynamics.

FAS-ligand regulates differential activation-induced cell death of human T-helper 1 and 17 cells in healthy donors and multiple sclerosis patients.

Functionally distinct T-helper (Th) subsets orchestrate immune responses. Maintenance of homeostasis through the tight control of inflammatory Th cells is crucial to avoid autoimmune inflammation. Activation-Induced Cell Death (AICD) regulates homeostasis of T cells, and it has never been investigated in human Th cells. We generated stable clones of inflammatory Th subsets involved in autoimmune diseases, such as Th1, Th17 and Th1/17 cells, from healthy donors (HD) and multiple sclerosis (MS) patients and we measured AICD. We find that human Th1 cells are sensitive, whereas Th17 and Th1/17 are resistant, to AICD. In particular, Th1 cells express high level of FAS-ligand (FASL), which interacts with FAS and leads to caspases' cleavage and ultimately to cell death. In contrast, low FASL expression in Th17 and Th1/17 cells blunts caspase 8 activation and thus reduces cell death. Interestingly, Th cells obtained from healthy individuals and MS patients behave similarly, suggesting that this mechanism could explain the persistence of inflammatory IL-17-producing cells in autoimmune diseases, such as MS, where their generation is particularly substantial.

Period doubling induced by thermal noise amplification in genetic circuits.

Rhythms of life are dictated by oscillations, which take place in a wide rage of biological scales. In bacteria, for example, oscillations have been proven to control many fundamental processes, ranging from gene expression to cell divisions. In genetic circuits, oscillations originate from elemental block such as autorepressors and toggle switches, which produce robust and noise-free cycles with well defined frequency. In some circumstances, the oscillation period of biological functions may double, thus generating bistable behaviors whose ultimate origin is at the basis of intense investigations. Motivated by brain studies, we here study an "elemental" genetic circuit, where a simple nonlinear process interacts with a noisy environment. In the proposed system, nonlinearity naturally arises from the mechanism of cooperative stability, which regulates the concentration of a protein produced during a transcription process. In this elemental model, bistability results from the coherent amplification of environmental fluctuations due to a stochastic resonance of nonlinear origin. This suggests that the period doubling observed in many biological functions might result from the intrinsic interplay between nonlinearity and thermal noise.

Structural disorder and anomalous diffusion in random packing of spheres.

Nowadays Nuclear Magnetic Resonance diffusion (dNMR) measurements of water molecules in heterogeneous systems have broad applications in material science, biophysics and medicine. Up to now, microstructural rearrangement in media has been experimentally investigated by studying the diffusion coefficient (D(t)) behavior in the tortuosity limit. However, this method is not able to describe structural disorder and transitions in complex systems. Here we show that, according to the continuous time random walk framework, the dNMR measurable parameter α, quantifying the anomalous regime of D(t), provides a quantitative characterization of structural disorder and structural transition in heterogeneous systems. To demonstrate this, we compare α measurements obtained in random packed monodisperse micro-spheres with Molecular Dynamics simulations of disordered porous media and 3D Monte Carlo simulation of particles diffusion in these kind of systems. Experimental results agree well with simulations that correlate the most used parameters and functions characterizing the disorder in porous media.

Acoustic dynamics of network-forming glasses at mesoscopic wavelengths.

The lack of long-range structural order in amorphous solids induces well known thermodynamic anomalies, which are the manifestation of distinct peculiarities in the vibrational spectrum. Although the impact of such anomalies vanishes in the long wavelength, elastic continuum limit, it dominates at length scales comparable to interatomic distances, implying an intermediate transition regime still poorly understood. Here we report a study of such mesoscopic domains by means of a broadband version of picosecond photo-acoustics, developed to coherently generate and detect hypersonic sound waves in the sub-THz region with unprecedented sampling efficiency. We identify a temperature-dependent fractal v(3/2) frequency behaviour of the sound attenuation, pointing to the presence of marginally stable regions and a transition between the two above mentioned limits. The essential features of this behaviour are captured by a theoretical approach based on random spatial variation of the shear modulus, including anharmonic interactions.

Dynamics and Thermodynamics beyond the critical point.

Sudden changes in the dynamical properties of a supercritical fluid model have been found as a function of pressure and temperature (T/T(c) = 2-5 and P/P(c) = 10-10(3)), striving with the notion of a single phase beyond the critical point established by thermodynamics. The sound propagation in the Terahertz frequency region reveals a sharp dynamic crossover between the gas like and the liquid like regimes along several isotherms, which involves, at sufficiently low densities, the interplay between purely acoustic waves and heat waves. Such a crossover allows one to determine a dynamic line in the phase diagram which exhibits a very tight correlation with a number of thermodynamic observables, showing that the supercritical state is remarkably more complex than thought so far.

Transport of self-propelling bacteria in micro-channel flow.

Understanding the collective motion of self-propelling organisms in confined geometries, such as that of narrow channels, is of great theoretical and practical importance. By means of numerical simulations we study the motion of model bacteria in 2D channels under different flow conditions: fluid at rest, steady and unsteady flow. We find aggregation of bacteria near channel walls and, in the presence of external flow, also upstream swimming, which turns out to be a very robust result. Detailed analysis of bacterial velocity and orientation fields allows us to quantify the phenomenon by varying cell density, channel width and fluid velocity. The tumbling mechanism turns out to have strong influence on velocity profiles and particle flow, resulting in a net upstream flow in the case of non-tumbling organisms. Finally we demonstrate that upstream flow can be enhanced by a suitable choice of an unsteady flow pattern.

Nonergodicity factor, fragility, and elastic properties of polymeric glassy sulfur.

We present a detailed investigation of the vibrational dynamics of glassy sulfur (g-S). The large frequency range spanned in this study has allowed us to carefully scrutinize the elastic properties of g-S and to analyze their relation to various features of both the glassy and the liquid state. In particular, the acoustic properties of g-S present a quasi-harmonic behavior in the THz frequency range, while at lower frequency, in the GHz range, they are affected by a strong anharmonic contribution. Moreover, the high frequency (THz) dynamics of g-S does not present signatures of the elastic anomalies recently observed in a number of glasses. Despite this apparent contradiction, we show that this finding is not in disagreement with the previous ones. Finally, by considering the correct long wavelength limit of the density fluctuations in the glassy state, we estimate the continuum limit of the nonergodicity factor and we investigate recently proposed relations between the fast dynamics of glasses and the slow dynamics of the corresponding viscous melts.

Spatio-temporal anomalous diffusion in heterogeneous media by nuclear magnetic resonance.

In this paper, we describe nuclear magnetic resonance measurements of water diffusion in highly confined and heterogeneous colloidal systems using an anomalous diffusion model. For the first time, temporal and spatial fractional exponents, α and µ, introduced within the framework of continuous time random walk, are simultaneously measured by pulsed gradient spin-echo NMR technique in samples of micro-beads dispersed in aqueous solution. In order to mimic media with low and high level of disorder, mono-dispersed and poly-dispersed samples are used. We find that the exponent α depends on the disorder degree of the system. Conversely, the exponent µ depends on both bead sizes and magnetic susceptibility differences within samples. The new procedure proposed here may be a useful tool to probe porous materials and microstructural features of biological tissue.

Acoustic dissipation and density of states in liquid, supercooled, and glassy glycerol.

Combined Brillouin spectra collected at visible, ultraviolet, and x-ray frequencies are used to reconstruct the imaginary part of the acoustic compliance J'' over a wide frequency range between 0.5 GHz and 5 THz. For liquid, supercooled, and glassy glycerol, J'' is found to be linearly dependent on the tagged-particle susceptibility measured by incoherent neutron scattering up to ≃1 THz, giving evidence of a clear relation between acoustic power dissipation and density of states. A simple but general formalism is presented to quantitatively explain this relation, thus clarifying the connection between the quasielastic component observed in neutron scattering experiments and the fast relaxation dynamics probed by Brillouin scattering.

Single-molecule imaging with x-ray free-electron lasers: dream or reality?

X-ray free-electron lasers (XFEL) are revolutionary photon sources, whose ultrashort, brilliant pulses are expected to allow single-molecule diffraction experiments providing structural information on the atomic length scale of nonperiodic objects. This ultimate goal, however, is currently hampered by several challenging questions basically concerning sample damage, Coulomb explosion, and the role of nonlinearity. By employing an original ab initio approach, we address these issues showing that XFEL-based single-molecule imaging will be only possible with a few-hundred long attosecond pulses, due to significant radiation damage and the formation of preferred multisoliton clusters which reshape the overall electronic density of the molecular system at the femtosecond scale.

Vibrational dynamics and surface structure of amorphous selenium.

In contrast to crystalline solids in which structural order governs dynamics and thermodynamics, the lack of long-range periodicity in amorphous materials is responsible for several anomalies. Although the relation between these anomalies and the 'bulk structure' is generally understood, the surface structure and the corresponding vibrational spectrum of amorphous solids is practically an unexplored theme. In this study, we resolve the differences in vibrational dynamics and atomic structure between bulk and surface (top 5 nm) atoms of amorphous selenium. We combine experimental (grazing incidence inelastic X-ray scattering) and computational (ab initio and semiempirical molecular orbital theoretical calculations) methods to scrutinize a variety of possible structural models. We find that a high concentration of particular types of 'coordination defects' in the surface layer is responsible for the observed differences. Resolving the structure of amorphous surfaces is, for example, important for understanding nanoparticles' properties where the surface-to-bulk ratio has a crucial role.