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Giancarlo Ruocco

Publications and source records attributed to Giancarlo Ruocco.

At least 37 records · Page 2Linked to original sources
arXiv2024

Consensus Statement on Brillouin Light Scattering Microscopy of Biological Materials

Brillouin Light Scattering (BLS) spectroscopy is a non-invasive, non-contact, label-free optical technique that can provide information on the mechanical properties of a material on the sub-micron scale. Over the last decade it has seen increased applications in the life sciences, driven by the observed significance of mechanical properties in biological processes, the realization of more sensitive BLS spectrometers and its extension to an imaging modality. As with other spectroscopic techniques, BLS measurements not only detect signals characteristic of the investigated sample, but also of the experimental apparatus, and can be significantly affected by measurement conditions. The aim of this consensus statement is to improve the comparability of BLS studies by providing reporting recommendations for the measured parameters and detailing common artifacts. Given that most BLS studies of biological matter are still at proof-of-concept stages and use different--often self-built--spectrometers, a consensus statement is particularly timely to assure unified advancement.

physics.optics↗
arXiv2024

Stochastically Structured Illumination Microscopy scan less super resolution imaging

In Super-resolution, a varying-illumination image stack is required. This enriched the dataset typically necessitates precise mechanical control and micron scale optical alignment and repeatability. Here, we introduce a novel methodology for super-resolution microscopy called Stochastically Structured Illumination Microscopy (S2IM), which bypasses the need for illumination control instead exploiting the random, uncontrolled movement of the target object. We tested our methodology within the clinically relevant ophthalmoscopic setting, harnessing the inherent saccadic motion of the eye to induce stochastic displacement of the illumination pattern on the retina. We opted to avoid human subjects by utilizing a phantom eye model, featuring a retina composed of human induced pluripotent stem cells (iPSC) retinal neurons, and replicating the ocular saccadic movements by custom actuators. Our findings demonstrate that S$^2$IM unlocks scan-less super-resolution with a resolution enhancement of 1.91, with promising prospects also beyond ophthalmoscopy applications such as active matter or atmospheric/astronomical observation.

physics.optics↗
arXiv2024

Probing leukemia cells behavior under starvation

The ability of a cancer cell population to achieve heterogeneity in their phenotype distributions offers advantages in tumor invasiveness and drug resistance. Studying the mechanisms behind such observed heterogeneity in mammalian cells presents challenges due for instance to the prolonged proliferation times compared to widely studied unicellular organisms like bacteria and yeast. Here, we studied the response of leukemia cell populations to serum starvation via a protocol, we recently developed, that makes use of live cell fluorescence and flow cytometry in combination with a quantitative analytical model to follow the population proliferation while monitoring the dynamics of its phenotype distributions. We found that upon switching between a serum-rich to a serum-poor media, leukemia cells (i) maintain a memory of the previous environment up to one generation even in the presence of severe medium-depletion, before (ii) adapting their growth and division rates to the novel environment while preserving a sizer-like division strategy. Finally, looking at the mitochondria content of the proliferating vs non-proliferating cells, we found that the latter is characterized by a higher number of older mitochondria, suggesting a possible functional role of the observed asymmetric partitioning of (aged) mitochondria in leukemia cells.

q-bio.CB↗
arXiv2024

Theory of elastic constants of athermal amorphous solids with internal stresses

A new microscopic derivation of the elastic constants of amorphous solids is presented within the framework of nonaffine lattice dynamics, which makes use of a perturbative form of the low-frequency eigenvectors of the dynamical matrix introduced in [V. Mazzacurati, G. Ruocco, M. Sampoli EPL 34, 681 (1996)]. The theory correctly recovers the shear modulus at jamming, $μ\sim (z-2d)$, including prefactors in quantitative agreement with simulations. Furthermore, this framework allows us, for the first time, to include the effect of internal stresses. The theory shows that the Maxwell rigidity criterion $z=2d$ is violated with internal stress. In particular, $μ\sim (z-2df)$ where $f<1$ if the bonds are, on average, stretched, and the solid is thus rigid below the Maxwell isostatic limit, while $f>1$ if the bonds are, on average, compressed. The coefficient $f$ is derived in analytical form and depends only on $d$ and on the average particle displacement from the interaction energy minimum.

cond-mat.soft↗
arXiv2024

Compact assessment of molecular surface complementarities enhances neural network-aided prediction of key binding residues

Predicting interactions between biomolecules, such as protein-protein complexes, remains a challenging problem. Despite the many advancements done so far, the performances of docking protocols are deeply dependent on their capability of identify binding regions. In this context, we present a novel approach that builds upon our previous works modeling protein surface patches via sets of orthogonal polynomials to identify regions of high shape/electrostatic complementarity. By incorporating another key binding property, such as the balance between hydrophilic and hydrophobic contributions, we define new binding matrices that serve an effective inputs for training a neural network. Our approach also allows for the quantitative definition of a typical binding site area - approximately 10Å~in radius - where hydrophobic contribution and shape complementarity, which reflects the Lennard-Jones interaction, are maximized. Using this new architecture, CIRNet (Core Interacting Residues Network), we achieve an accuracy of approximately 0.82 in identifying pairs of core interacting residues on a balanced dataset. In a blind search for core interacting residues, CIRNet distinguishes these from decoys with a ROC AUC of 0.72. This protocol can enahnce docking algorithms by rescaling the proposed poses. When applied to the top ten models from three popular docking server, CIRNet improves docking outcomes, reducing the the average RMSD between the refined poses and the native state by up to 58%.

q-bio.BM↗
arXiv2024

Zepyros: A webserver to evaluate the shape complementarity of protein-protein interfaces

Shape complementarity of molecular surfaces at the interfaces is a well-known characteristic of protein-protein binding regions, and it is critical in influencing the stability of the complex. Measuring such complementarity is at the basis of methods for both the prediction of possible interactions and for the design/optimization of speficic ones. However, only a limited number of tools are currently available to efficiently and rapidly assess it. Here, we introduce Zepyros, a webserver for fast measuring of the shape complementarity between two molecular interfaces of a given protein-protein complex using structural information. Zepyros is implemented as a publicly available tool with a user-friendly interface. Our server can be found at the following link (all major browser supported): https://zepyros.bio-groups.com

q-bio.QM↗
arXiv2023

High throughput interactome determination via sulfur anomalous scattering

We propose a novel approach to detect the binding between proteins making use of the anomalous diffraction of natively present heavy elements inside the molecule 3D structure. In particular, we suggest considering sulfur atoms contained in protein structures at lower percentages than the other atomic species. Here, we run an extensive preliminary investigation to probe both the feasibility and the range of usage of the proposed protocol. In particular, we (i) analytically and numerically show that the diffraction patterns produced by the anomalous scattering of the sulfur atoms in a given direction depend additively on the relative distances between all couples of sulfur atoms. Thus the differences in the patterns produced by bound proteins with respect to their non-bonded states can be exploited to rapidly assess protein complex formation. Next, we (ii) carried out analyses on the abundances of sulfurs in the different proteomes and molecular dynamics simulations on a representative set of protein structures to probe the typical motion of sulfur atoms. Finally, we (iii) suggest a possible experimental procedure to detect protein-protein binding. Overall, the completely label-free and rapid method we propose may be readily extended to probe interactions on a large scale even between other biological molecules, thus paving the way to the development of a novel field of research based on a synchrotron light source.

physics.bio-ph↗
arXiv2023

Determining cancer cells division strategy

Heterogeneity in the size distribution of cancer cell populations has been recently linked to drug resistance and invasiveness. However, despite many progresses have been made in understanding how such heterogeneous size distributions arise in fast-proliferating cell types -like bacteria and yeast-, comprehensive investigations on cancer cell populations are still lacking mainly due to the difficulties of monitoring the proliferation of the time scales typical of mammalian cells. From a reductionist cell dynamics point of view, the strategies allowing size homeostasis are roughly grouped into three classes, \emph{i.e.} timer, sizer, or adder. These strategies are empirically distinguishable given the phenomenological measurable relationship between the cell size at birth and at division, which requires following the proliferation at the single-cell level. Here, we show how it is possible to infer the growth regime and division strategy of leukemia cell populations using live cell fluorescence labeling and flow cytometry in combination with a quantitative analytical model where both cell growth and division rates depend on powers of the cell size. Using our novel approach, we found that the dynamics of the size distribution of leukemia Jurkat T-cells is quantitatively reproduced by (i) a sizer-like division strategy, with (ii) division times following an Erlang distribution given by the sum of at least three independent exponentially-distributed times and (iii) fluctuations up to 15\% of the inherited fraction of size at division with respect to the mother cell size. Finally, we note that our experimental and theoretical apparatus can be easily extended to other cell types and environmental conditions, allowing for a comprehensive characterization of the growth and division model different cells can adopt.

q-bio.CB↗
arXiv2023

The nature of non-phononic excitations in disordered systems

Using heterogeneous-elasticity theory (HET) and a generalisation of HET theory (GHET), obtained by applying a newly developed procedure for obtaining the continuum limit of the glass's Hessian, we investigate the nature of vibrational excitations, which are present in small systems, which do not allow for low-frequency phonons. We identify two types of such non-phononic excitations. In marginally stable systems, which can be prepared by quenching from a rather high parental temperature, the low-frequency regime is dominated by random-matrix vibrational wavefunctions (type-I) which in macroscopic samples gives rise to the boson peak. They show a density of states (DOS), which scales as $g(ω)\sim ω^2$. In more stable systems (reached by a somewhat lower parental temperature) a gap appears in the type-I spectrum. This gap is filled with other type-II non-phononic excitations, which are not described by the previous version of HET, and have a DOS, which scales as $g(ω)\simω^s$ with $3<s<5$. Using GHET we demonstrate that the type-II excitations are due to local non-irrotational oscillations associated with the stress field. The frequency scaling exponent $s$ turns out to be non-universal, depending on the details of the interaction potential. Specifically, we demonstrate that $s$ depends on the statistics of the small values of the local frozen-in stresses, which are, in turn, governed by the shape of the pair potential close to values where the potential or its first derivative vanishes. All these findings are verified by extensive numerical simulations of small soft-sphere glasses. Further, using level-distance statistics, we demonstrate that both types of non-phononic excitations obey the Gaussian-Orthogonal-Ensemble random-matrix statistics, which means that they are extended and not localized.

cond-mat.dis-nn↗
arXiv2023

Dichotomic Aging Behaviour in a Colloidal Glass

An unexpected dichotomic long time aging behaviour is observed in a glassy colloidal clay suspension investigated by X-Ray Photon Correlation Spectroscopy and Dynamic Light Scattering. In the long time aging regime the intensity autocorrelations are non-exponential, following the Kohlrausch-Williams-Watts functional form with exponent bQ. We show that for spontaneously aged samples a stretched behaviour (β_Q < 1) is always found. Surprisingly a compressed exponent (β_Q > 1) appears only when the system is rejuvenated by application of a shear field. In both cases the relaxation times scale as Q^{-1}. These observations shed light on the origin of compressed exponential behaviour and helps in classifying previous results in the literature on anomalous dynamics.

cond-mat.soft↗
arXiv2023

Structural and microscopic relaxations in a colloidal glass

The aging dynamics of a colloidal glass has been studied by multiangle Dynamic Light Scattering, Neutron Spin Echo, X-ray Photon Correlation Spectroscopy and Molecular Dynamics simulations. The two relaxation processes, microscopic (fast) and structural (slow), have been investigated in an unprecedentedly wide range of time and length scales covering both ergodic and nonergodic regimes. The microscopic relaxation time remains diffusive at all length scales across the glass transition scaling with wavevector Q as Q^{-2}. The length-scale dependence of structural relaxation time changes from diffusive, characterized by a Q^{-2}-dependence in the early stages of aging, to Q^{-1}- dependence in the full aging regime which marks a discontinuous hopping dynamics. Both regimes are associated with a stretched behaviour of the correlation functions. We expect these findings to provide a general description of both relaxations across the glass transition.

cond-mat.soft↗
arXiv2023

Photonic Stochastic Emergent Storage: Exploiting Scattering-intrinsic Patterns for Programmable Deep Classification

Disorder is a pervasive characteristic of natural systems, offering a wealth of non-repeating patterns. In this study, we present a novel storage method that harnesses naturally-occurring random structures to store an arbitrary pattern in a memory device. This method, the stochastic emergent storage (SES), builds upon the concept of emergent archetypes, where a training set of imperfect examples (prototypes) is employed to instantiate an archetype in an Hopfield-like network through emergent processes. We demostrate this non-Hebbian paradigm in the photonic domain by utilizing random transmission matrices, which govern light scattering in a white-paint turbid medium, as prototypes. Through the implementation of programmable hardware, we successfully realize and experimentally validate the capability to store an arbitrary archetype and perform classification at the speed of light. Leveraging the vast number of modes excited by mesoscopic diffusion, our approach enables the simultaneous storage of thousands of memories without requiring any additional fabrication efforts. Similar to a content addressable memory, all stored memories can be collectively assessed against a given pattern to identify the matching element. Furthermore, by organizing memories spatially into distinct classes, they become features within a higher-level categorical (deeper) optical classification layer.

cond-mat.dis-nn↗
arXiv2023

Osmolyte-Induced Protein Stability Changes Explained by Graph Theory

Enhanced stabilisation of protein structures via the presence of inert excipients is a key mechanism adopted both by physiological systems and in biotechnological applications. While the intrinsic stability of proteins is ultimately fixed by their amino acid composition and organisation, the interactions between excipients and proteins together with their concentrations introduce an additional layer of complexity and in turn, method of modulating protein stability. Here, we combined experimental measurements with molecular dynamics simulations and graph-theory based analyses to assess the stabilising/destabilising effects of different kinds of osmolytes on proteins during heat-mediated denaturation. We found that (i) proteins in solution with stability-enhancing osmolytes tend to have more compact interaction networks than those assumed in presence of destabilising excipients; (ii) a strong negative correlation (R = -0.85) characterises the relationship between the melting temperature Tm and the preferential interaction coefficient defined by the radial distribution functions of osmolytes and water around the protein and (iii) a positive correlation exists between osmolyte-osmolyte clustering and the extent of preferential exclusion from the local domain of the protein, suggesting that exclusion may be driven by enhanced steric hindrance of aggregated osmolytes.

q-bio.BM↗
arXiv2023

Diffusion of light in turbid media and Kubelka-Munk theory

We show that the Kubelka-Munk equations for the description of the intensity transfer of light in turbid media are equivalent to a one-dimensional diffusion equation, which is obtained by averaging the three-dimensional diffusion equation over the lateral directions. This enables us to identify uniquely the Kubelka-Munk parameters and derive expressions for diffuse reflection and transmission coefficients including the effect of internal reflections. Without internal reflections we recover the Kubelka-Munk formulas for these coefficients. We show that the Kubelka-Munk equations are the proper radiative-transfer equations for the one-dimensional diffusion problem and comment on previous attempts to derive the Kubelka-Munk equations.

cond-mat.dis-nn↗
arXiv2023

The electric and magnetic disordered Maxwell equations as eigenvalue problem

We consider Maxwell's equations in a 3-dimensional material, in which both, the electric permittivity, as well as the magnetic permeability, fluctuate in space. Differently from all previous treatments of the disordered electromagnetic problem, we transform Maxwell's equations and the electric and magnetic fields in such a way that the linear operator in the resulting secular equations is manifestly Hermitian, in order to deal with a proper eigenvalue problem. As an application of our general formalism, we use an appropriate version of the Coherent-Potential approximation (CPA) to calculate the photon density of states and scattering-mean-free path. Applying standard localization theory, we find that in the presence of both electric and magnetic disorder the spectral range of Anderson localization appears to be much larger than in the case of electric (or magnetic) disorder only. Our result could explain the absence of experimental evidence of 3D Anderson localization of light (all the existing experiments has been performed with electric disorder only) and pave the way towards a successful search of this, up to now, elusive phenomenon.

physics.optics↗
arXiv2023

Instantaneous normal modes in liquids: a heterogeneous-elastic-medium approach

The concept of vibrational density of states in glasses has been mirrored in liquids by the instantaneous-normal-mode spectrum. While in glasses instantaneous configurations correspond to minima of the potential-energy hypersurface and all eigenvalues of the associated Hessian matrix are therefore positive, in liquids this is no longer true, and modes corresponding to both positive and negative eigenvalues exist. The instantaneous-normal-mode spectrum has been numerically investigated in the past, and it has been demonstrated to bring important information on the liquid dynamics. A systematic deeper theoretical understanding is now needed. Heterogeneous-elasticity theory has proven to be successful in explaining many details of the low-frequency excitations in glasses, ranging from the thoroughly studied boson peak, down to the more elusive non-phononic excitations observed in numerical simulations at the lowest frequencies. Here we present an extension of heterogeneous-elasticity theory to the liquid state, and show that the outcome of the theory agrees well to the results of extensive molecular-dynamics simulations of a model liquid at different temperatures. We show that the spectral shape strongly depends on temperature, being symmetric at high temperatures and becoming rather asymmetric at low temperatures, close to the dynamical critical temperature. Most importantly, we demonstrate that the theory naturally reproduces a surprising phenomenon, a zero-energy spectral singularity with a cusp-like character developing in the vibrational spectra upon cooling. This feature, known from a few previous numerical studies, has been generally overlooked in the past due to a misleading representation of the data. We provide a thorough analysis of this issue, based on both very accurate predictions of our theory, and computational studies of model liquid systems with extended size.

cond-mat.dis-nn↗
arXiv2022

Hopfield-like open channel retrieval for disordered optical media

The measurement of the optical Transmission Matrix (TM) enables to access "open channels": input patterns, specific to each scattering structure, capable to deliver very high transmission. Various approaches, based either on multiple interferometric measurements or on systematic random testing of incident wavefronts, enable to estimate the inputs required to excite these open channels. Here, we provide for the first time an approach enabling the complete and reference-less retrieval of the open channels. It is based on the full mapping all the pairwise interference terms resulting from all the input modes couples. We show that these interference terms are organized into a bi-dyadic coupling matrix whose eigenvalues enables to access the open channel. A disordered optical system, is thus behaving exactly like an Hopfield neural network, where a specific input vector (an eigenvalue of the neurons' coupling matrix) enables to retrieve a specific memory pattern. The proposed Hopfield like open-channel-retrieval approach, enables to reach almost 100$\%$ of the theoretically expected value of the Intensity. Moreover employing a digital micromirror device to modulate light, we demonstrate high speed laser scanning at the back of a disordered medium.

physics.optics↗
arXiv2022

Retinal fluorescence microscopy in artificial ophthalmic environment: the Humanized Phantom Eye

Phantom eye devices are designed to mimic the optical properties of the human eye; however, the retinal structures are typically emulated with synthetic tissues. Thus, it is currently impossible to exploit phantom eye devices for fluorescence microscopy experiments on cultures, or ex-vivo tissues, although these ophthalmic measurements would be of importance for many applications such as the testing of retinal biomarkers. Here we report and describe the development of a phantom eye designed to host biological samples, such as retinal cultures differentiated from human induced pluripotent stem cells. We characterized the imaging performance of the humanized phantom eye on standard biomarkers such as Alexa Fluor 532 and Alexa fluor 594.

physics.med-ph↗