arXiv subjects

Giancarlo Ruocco

Publications and source records attributed to Giancarlo Ruocco.

At least 73 records · Page 4Linked to original sources

arXiv2020

In-Silico evidence for two receptors based strategy of SARS-CoV-2

We propose a novel numerical method able to determine efficiently and effectively the relationship of complementarity between portions of proteins surfaces. This innovative and general procedure, based on the representation of the molecular iso-electron density surface in terms of 2D Zernike polynomials, allows the rapid and quantitative assessment of the geometrical shape complementarity between interacting proteins, that was unfeasible with previous methods. We first tested the method with a large dataset of known protein complexes obtaining an overall area under the ROC curve of 0.76 in the blind recognition of binding sites and then applied it to investigate the features of the interaction between the Spike protein of SARS-Cov-2 and human cellular receptors. Our results indicate that SARS-CoV-2 uses a dual strategy: its spike protein could also interact with sialic acid receptors of the cells in the upper airways, in addition to the known interaction with Angiotensin-converting enzyme 2.

physics.bio-ph↗

arXiv2020

On the number of limit cycles in diluted neural networks

We consider the storage properties of temporal patterns, i.e. cycles of finite lengths, in neural networks represented by (generally asymmetric) spin glasses defined on random graphs. Inspired by the observation that dynamics on sparse systems have more basins of attractions than the dynamics of densely connected ones, we consider the attractors of a greedy dynamics in sparse topologies, considered as proxy for the stored memories. We enumerate them using numerical simulation and extend the analysis to large systems sizes using belief propagation. We find that the logarithm of the number of such cycles is a non monotonic function of the mean connectivity and we discuss the similarities with biological neural networks describing the memory capacity of the hippocampus.

cond-mat.dis-nn↗

arXiv2019

Simulated Epidemics in 3D Protein Structures to Detect Functional Properties

The outcome of an epidemic is closely related to the network of interactions between the individuals. Likewise, protein functions depend on the 3D arrangement of their residues and on the underlying energetic interaction network. Borrowing ideas from the theoretical framework that has been developed to address the spreading of real diseases, we study the diffusion of a fictitious epidemic inside the protein non-bonded interaction network. Our approach allowed to probe the overall stability and the capability to propagate information in the complex 3D-structures and proved to be very efficient in addressing different problems, from the assessment of thermal stability to the identification of allosteric sites.

q-bio.BM↗

arXiv2019

Relation between heterogeneous frozen regions in supercooled liquids and non-Debye spectrum in the corresponding glasses

Recent numerical studies on glassy systems provide evidences for a population of non-Goldstone modes (NGMs) in the low-frequency spectrum of the vibrational density of states $D(ω)$. Similarly to Goldstone modes (GMs), i. e., phonons in solids, NGMs are soft low-energy excitations. However, differently from GMs, NGMs are localized excitations. Here we first show that the parental temperature $T^*$ modifies the GM/NGM ratio in $D(ω)$. In particular, the phonon attenuation is reflected in a parental temperature dependency of the exponent $s(T^*)$ in the low-frequency power law $D(ω) \sim ω^{s(T^*)}$, with $2 \leq s(T^*) \leq 4 $. Secondly, by comparing $s(T^*)$ with $s(p)$, i. e., the same quantity obtained by pinning \mttp{a} $p$ particle fraction, we suggest that $s(T^*)$ reflects the presence of dynamical heterogeneous regions of size $ξ^3 \propto p$. Finally, we provide an estimate of $ξ$ as a function of $T^*$, finding a mild power law divergence, $ξ\sim (T^* - T_d)^{-α/3}$, with $T_d$ the dynamical crossover temperature and $α$ falling in the range $α\in [0.8,1.0]$.

cond-mat.dis-nn↗

arXiv2019

Rayleigh anomalies and disorder-induced mixing of polarizations at nanoscale in amorphous solids. Testing 1-octyl-3-methylimidazolium chloride glass

Acoustic excitations in topologically disordered media at mesoscale present anomalous features with respect to the Debye's theory. In a three-dimensional medium an acoustic excitation is characterized by its phase velocity, intensity and polarization. The so-called Rayleigh anomalies, which manifest in attenuation and retardation of the acoustic excitations, affect the first two properties. The topological disorder is, however, expected to influence also the third one. Acoustic excitations with a well-defined polarization in the continuum limit present indeed a so-called mixing of polarizations at nanoscale, as attested by experimental observations and Molecular Dynamics simulations. We provide a comprehensive experimental characterization of acoustic dynamics properties of a selected glass, 1-octyl-3-methylimidazolium chloride glass, whose heterogeneous structure at nanoscale is well-assessed. Distinctive features, which can be related to the occurrence of the Rayleigh anomalies and of the mixing of polarizations are observed. We develop, in the framework of the Random Media Theory, an analytical model that allows a quantitative description of all the Rayleigh anomalies and the mixing of polarizations. Contrast between theoretical and experimental features for the selected glass reveals an excellent agreement. The quantitative theoretical approach permits thus to demonstrate how the mixing of polarizations generates distinctive feature in the dynamic structure factor of glasses and to unambiguously identify them. The robustness of the proposed theoretical approach is validated by its ability to describe as well transverse acoustic dynamics.

cond-mat.dis-nn↗

arXiv2019

On the number of limit cycles in asymmetric neural networks

The comprehension of the mechanisms at the basis of the functioning of complexly interconnected networks represents one of the main goals of neuroscience. In this work, we investigate how the structure of recurrent connectivity influences the ability of a network to have storable patterns and in particular limit cycles, by modeling a recurrent neural network with McCulloch-Pitts neurons as a content-addressable memory system. A key role in such models is played by the connectivity matrix, which, for neural networks, corresponds to a schematic representation of the "connectome": the set of chemical synapses and electrical junctions among neurons. The shape of the recurrent connectivity matrix plays a crucial role in the process of storing memories. This relation has already been exposed by the work of Tanaka and Edwards, which presents a theoretical approach to evaluate the mean number of fixed points in a fully connected model at thermodynamic limit. Interestingly, further studies on the same kind of model but with a finite number of nodes have shown how the symmetry parameter influences the types of attractors featured in the system. Our study extends the work of Tanaka and Edwards by providing a theoretical evaluation of the mean number of attractors of any given length $L$ for different degrees of symmetry in the connectivity matrices.

cond-mat.dis-nn↗

arXiv2019

Brillouin microscopy - a revolutionary tool for mechanobiology?

The role and importance of mechanical properties of cells and tissues in cellular function, development as well as disease has widely been acknowledged, however standard techniques currently used to assess them exhibit intrinsic limitations. Recently, a new type of optical elastography, namely Brillouin microscopy, has emerged as a non-destructive, label- and contact-free method which can probe the viscoelastic properties of biological samples with diffraction-limited resolution in 3D. This has led to increased attention amongst the biological and medical research communities, but also to debates about the interpretation and relevance of the measured physical quantities. Here, we review this emerging technology by describing the underlying biophysical principles and discussing the interpretation of Brillouin spectra arising from heterogeneous biological matter. We further elaborate on the technique's limitations as well as its potential for new insights in biology in order to guide interested researchers from various fields.

physics.bio-ph↗

arXiv2018

The mixing of polarizations in the acoustic excitations of disordered media with local isotropy

An approximate solution of the Dyson equation related to a stochastic Helmholtz equation, which describes the acoustic dynamics of a three-dimensional isotropic random medium with elastic tensor fluctuating in space, is obtained in the framework of the Random Media Theory. The wavevector-dependence of the self-energy is preserved, thus allowing a description of the acoustic dynamics at wavelengths comparable with the size of heterogeneity domains. This in turn permits to quantitatively describe the mixing of longitudinal and transverse dynamics induced by the medium's elastic heterogeneity and occurring at such wavelengths. A functional analysis aimed to attest the mathematical coherence and to define the region of validity in the frequency-wavevector plane of the proposed approximate solution is presented, with particular emphasis dedicated to the case of disorder characterized by an exponential decay of the covariance function.

cond-mat.dis-nn↗

arXiv2018

Scattering Assisted Imaging

An ideal imaging system provides a spatial resolution that is ultimately dictated by the numerical aperture (NA) of the illumination and collection optics. In biological tissue, resolution is further affected by scattering limiting the penetration depth to a few tenths of microns. Here, we exploit the properties of speckle patterns embedded into a strongly scattering matrix to generate a high-resolution illumination. Combining adaptive optics with a custom deconvolution algorithm, we obtain an increase in the transverse spatial resolution by a factor of 2.5 with respect to the diffraction limit. This Scattering Assisted Imaging (SAI) is compatible with long working distance optics and perfectly works on tissue, potentially paving the way to bulk imaging in turbid samples.

physics.optics↗

arXiv2018

Effect of dilution in asymmetric recurrent neural networks

We study with numerical simulation the possible limit behaviors of synchronous discrete-time deterministic recurrent neural networks composed of N binary neurons as a function of a network's level of dilution and asymmetry. The network dilution measures the fraction of neuron couples that are connected, and the network asymmetry measures to what extent the underlying connectivity matrix is asymmetric. For each given neural network, we study the dynamical evolution of all the different initial conditions, thus characterizing the full dynamical landscape without imposing any learning rule. Because of the deterministic dynamics, each trajectory converges to an attractor, that can be either a fixed point or a limit cycle. These attractors form the set of all the possible limit behaviors of the neural network. For each network, we then determine the convergence times, the limit cycles' length, the number of attractors, and the sizes of the attractors' basin. We show that there are two network structures that maximize the number of possible limit behaviors. The first optimal network structure is fully-connected and symmetric. On the contrary, the second optimal network structure is highly sparse and asymmetric. The latter optimal is similar to what observed in different biological neuronal circuits. These observations lead us to hypothesize that independently from any given learning model, an efficient and effective biologic network that stores a number of limit behaviors close to its maximum capacity tends to develop a connectivity structure similar to one of the optimal networks we found.

cond-mat.dis-nn↗

arXiv2018

Hyperuniformity in amorphous speckle patterns

Hyperuniform structures possess the ability to confine and drive light, although their fabrication is extremely challenging. Here we demonstrate that speckle patters obtained by a superposition of randomly arranged sources of Bessel beams can be used to generate hyperunifrom scalar fields. By exploiting laser light tailored with a spatial filter, we experimentally produce (without requiring any computational power) a speckle pattern possessing maxima at locations corresponding to a hyperuniform distribution. By properly filtering out intensity fluctuation from the same speckle pattern, it is possible to retrieve an intensity profile satisfying the hyperuniformity requirements. Our findings are supported by extensive numerical simulations.

physics.optics↗

arXiv2018

Probing the non-Debye low frequency excitations in glasses through random pinning

We investigate the properties of the low-frequency spectrum in the density of states $D(ω)$ of a three-dimensional model glass former. To magnify the Non-Debye sector of the spectrum, we introduce a random pinning field that freezes a finite particle fraction in order to break the translational invariance and shifts all the vibrational frequencies of the extended modes towards higher frequencies. We show that Non-Debye soft localized modes progressively emerge as the fraction $p$ of pinned particles increases. Moreover, the low-frequency tail of $D(ω)$ goes to zero as a power law $ω^{δ(p)}$, with $2 \!\leq \! δ(p) \!\leq\!4$ and $δ\!=\!4$ above a threshold fraction $p_{th}$.

cond-mat.dis-nn↗

arXiv2017

What is the right theory for Anderson localization of light?

Anderson localization of light is traditionally described in analogy to electrons in a random potential. Within this description the disorder strength -- and hence the localization characteristics -- depends strongly on the wavelength of the incident light. In an alternative description in analogy to sound waves in a material with spatially fluctuating elastic moduli this is not the case. Here, we report on an experimentum crucis in order to investigate the validity of the two conflicting theories using transverse-localized optical devices. We do not find any dependence of the observed localization radii on the light wavelength. We conclude that the modulus-type description is the correct one and not the potential-type one. We corroborate this by showing that in the derivation of the traditional, potential-type theory a term in the wave equation has been tacititly neglected. In our new modulus-type theory the wave equation is exact. We check the consistency of the new theory with our data using a field-theoretical approach (nonlinear sigma model).

physics.optics↗

arXiv2015

Theory of heterogeneous viscoelasticity

We review a new theory of viscoelasticity of a glass-forming viscous liquid near and below the glass transition. In our model we assume that each point in the material has a specific viscosity, which varies randomly in space according to a fluctuating activation free energy. We include a Maxwellian elastic term and assume that the corresponding shear modulus fluctuates as well with the same distribution as that of the activation barriers. The model is solved in coherent-potential approximation (CPA), for which a derivation is given. The theory predicts an Arrhenius-type temperature dependence of the viscosity in the vanishing-frequency limit, independent of the distribution of the activation barriers. The theory implies that this activation energy is generally different from that of a diffusing particle with the same barrier-height distribution. If the distribution of activation barriers is assumed to have Gaussian form, the finite-frequency version of the theory describes well the typical low-temperature alpha relaxation peak of glasses. Beta relaxation can be included by adding another Gaussian with center at much lower energies than that responsible for the alpha relaxation. At high frequencies our theory reduces to the description of an elastic medium with spatially fluctuating elastic moduli (heterogeneous elasticity theory), which explains the occurrence of the boson-peak-related vibrational anomalies of glasses.

cond-mat.dis-nn↗

arXiv2012

A stroll in the energy landscape

We review recent results on the potential energy landscape (PES) of model liquids. The role of saddle-points in the PES in connecting dynamics to statics is investigated, confirming that a change between minima-dominated and saddle-dominated regions of the PES explored in equilibrium happens around the Mode Coupling Temperature. The structure of the low-energy saddles in the basins is found to be simple and hierarchically organized; the presence of saddles nearby in energy to the local minima indicates that, at non-cryogenic temperatures, entropic bottlenecks limit the dynamics.

cond-mat.soft↗

arXiv2010

Molecular imaging with X-ray free electron lasers: dream or reality?

X-ray Free Electron Lasers (XFEL) are revolutionary photons sources, whose ultrashort, brilliant pulses are expected to allow single molecule diffraction experiments providing structural information on the atomic length scale. 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 \emph{ab-initio} approach, as well as exceptional resources of parallel computing, we address these issues showing that accurate XFEL-based single molecule imaging will be only possible with ultrashort pulses of half of femtosecond, due to significant radiation damage and the formation of preferred multi-soliton clusters which reshape the overall electronic density of the molecular system at the femtosecond scale.

physics.optics↗

arXiv2009

Generalized fluctuation-dissipation relation and effective temperature in off-equilibrium colloids

The fluctuation-dissipation relation (FDR), a fundamental result of equilibrium statistical physics, ceases to be valid when a system is taken out of the equilibrium. A generalization of FDR has been theoretically proposed for out-of-equilibrium systems: the kinetic temperature entering FDR is substituted by a time-scale dependent effective temperature. We combine the measurements of the correlation function of the rotational dynamics of colloidal particles obtained via dynamic light scattering with those of the birefringence response to study the generalized FDR in an off-equilibrium clay suspension undergoing aging. We i) find that FDR is strongly violated in the early stage of the aging process and is gradually recovered as the aging time increases and, ii), we determine the aging time evolution of the effective temperature, giving support to the proposed generalization scheme.

cond-mat.soft↗

arXiv2009

Time-dependent Nonlinear Optical Susceptibility of an Out-of-Equilibrium Soft Material

We investigate the time-dependent nonlinear optical absorption of a clay dispersion (Laponite) in organic dye (Rhodamine B) water solution displaying liquid-arrested state transition. Specifically, we determine the characteristic time $τ_D$ of the nonlinear susceptibility build-up due as to the Soret effect. By comparing $τ_D$ with the relaxation time provided by standard dynamic light scattering measurements we report on the decoupling of the two collective diffusion times at the two very different length scales during the aging of the out-of-equilibrium system. With this demonstration experiment we also show the potentiality of nonlinear optics measurements in the study of the late stage of arrest in soft materials.

cond-mat.soft↗