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One of the fundamental quantities in dynamics of the liquid state, the adiabatic speed of sound c s , is extremely difficult to predict from computer simulations, especially in ab initio simulations. Here we derive an expression for the instantaneous correlator of fluctuations of longitudinal component of stress tensor, which contains c s along with others quantities easy accessible via classical and ab initio computer simulations. We show that the proposed methodology works well in the case of Lennard-Jones and soft-sphere simple fluids, Kr–Ar liquid mixture in connection with simulations with effective pair interactions as well as for liquid Sb, fluid Hg and molten NaCl from ab initio simulations. [ABSTRACT FROM AUTHOR]

One of the fundamental quantities in dynamics of the liquid state, the adiabatic speed of sound c s , is extremely difficult to predict from computer simulations, especially in ab initio simulations. Here we derive an expression for the instantaneous correlator of fluctuations of longitudinal component of stress tensor, which contains c s along with others quantities easy accessible via classical and ab initio computer simulations. We show that the proposed methodology works well in the case of Lennard-Jones and soft-sphere simple fluids, Kr–Ar liquid mixture in connection with simulations with effective pair interactions as well as for liquid Sb, fluid Hg and molten NaCl from ab initio simulations. [ABSTRACT FROM AUTHOR]

We present ab initio simulations of a large system of 2400 particles of molten NaCl to investigate the behavior of collective mode dispersion beyond the hydrodynamic regime. In particular, we aim to explain the unusually strong increase in the apparent speed of sound with wave number, which significantly exceeds the typical positive sound dispersion of 10%–25% observed in simple liquids. We compare dispersions of "bare" acoustic and optic modes in NaCl with ab initio simulations of other ionic melts such as CuCl and LiBr, metallic liquid alloys such as Pb44Bi56 and Li4Tl, and the regular Lennard-Jones KrAr liquid simulated by classical molecular dynamics. Analytical expressions for the "bare" acoustic and optic branches of collective excitations help us to identify the impact of the high-frequency optic branch on the emergence of "fast sound" in binary melts. Our findings show that in ionic melts, the high-frequency speed of sound is much larger than in the simple Lennard-Jones liquids and metallic melts, leading to an observed strong viscoelastic increase in the apparent speed of sound—more than double its adiabatic value. [ABSTRACT FROM AUTHOR]

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, 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 the 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 centre at much lower energies than that is 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. [ABSTRACT FROM PUBLISHER]

Since decades, the concept of vibrational density of states in glasses has been mirrored in liquids by the instantaneous-normal-mode spectrum. In glasses instantaneous configurations are believed to be situated close to minima of the potential-energy hypersurface and all eigenvalues of the associated Hessian matrix are 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 and transport properties. A systematic deeper theoretical understanding is now needed. Heterogeneous-elasticity theory has proven to be particularly successful in explaining many details of the low-frequency excitations in glasses, ranging from the thoroughly studied boson peak, to other anomalies related to the crossover between wave-like and random-matrix-like excitations. 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 find that the spectrum of eigenvalues ρ (λ) has a sharp maximum close to (but not at) λ = 0 , and decreases monotonically with | λ | on both its stable and unstable side. 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. [ABSTRACT FROM AUTHOR]

We present a heterogeneous version of Maxwell's theory of viscoelasticity based on the assumption of spatially fluctuating local viscoelastic coefficients. The model is solved in coherent-potential approximation. The theory predicts an Arrhenius-type temperature dependence of the viscosity in the vanishing-frequency limit, independent of the distribution of the activation energies. It is shown that this activation energy is generally different from that of a diffusing particle with the same barrier-height distribution, which explains the violation of the Stokes-Einstein relation observed frequently in glasses. At finite but low frequencies, the theory describes low-temperature asymmetric alpha relaxation. As examples, we report the good agreement obtained for selected inorganic, metallic, and organic glasses. At high frequencies, the theory reduces to heterogeneous elasticity theory, which explains the occurrence of the boson peak and related vibrational anomalies. [ABSTRACT FROM AUTHOR]

A new methodology of calculation of dispersion and damping of collective excitations fromab initiomolecular dynamics (AIMD) of liquid metals is proposed. It is suggested to use for the analysis of AIMD-derived time correlation functions a thermo-viscoelastic dynamic model within an approach of the generalised collective modes. The proposed scheme, in which the viscoelastic matrix elements of the generalised hydrodynamic matrix are directly calculated from AIMD and the matrix elements requiring knowledge of energy density fluctuations in the system are treated as fitting parameters, allows to recover AIMD time correlation functions in a wide range of wave numbers. The dispersion and damping of collective excitations are obtained as a complex-conjugated pair of the generalised hydrodynamic matrix. An issue of sum rules in the proposed scheme is discussed. The methodology is applied for calculations of dispersion and damping of generalised acoustic modes in molten lithium. [ABSTRACT FROM AUTHOR]

Abstract: We report scaling results on the world’s largest supercomputer of our recently developed Billions-Body Molecular Dynamics (BBMD) package, which was especially designed for massively parallel simulations of the short-range atomic dynamics in structural glasses and amorphous materials. The code was able to scale up to 72 racks of an IBM BlueGene/P, with a measured 89% efficiency for a system with 100 billion particles. The code speed, with 0.13s per iteration in the case of 1 billion particles, paves the way to the study of billion-body structural glasses with a resolution increase of two orders of magnitude with respect to the largest simulation ever reported. We demonstrate the effectiveness of our code by studying the liquid–glass transition of an exceptionally large system made by a binary mixture of 1 billion particles. [Copyright &y& Elsevier]

Dispersion and damping of collective excitations in supercritical argon along the isothermal line of 280 K are studied by a combination of molecular dynamics simulations and Generalized Collective Mode (GCM) analysis. ‘Positive dispersion’ of collective excitations and its dependence on density is discussed on the basis of GCM theory of ‘positive dispersion’. [ABSTRACT FROM AUTHOR]

Abstract: An overview of the relaxation dynamics in simple liquids is undertaken, in view of the recent experimental results achieved by means of inelastic X-ray and neutron scattering. We address some basic issues related to the extension of ordinary hydrodynamic in the Thz domain, such as the coupling of density and entropy fluctuations and the origin of anomalous acoustic dispersion within the general context of disordered systems dynamics. Specifically, we show that the Landau Placzeck ratio do not describe the quasielastic component of the dynamic structure factor and that the positive dispersion is a universal feature which can be understood in terms of a disorder induced relaxation process. [Copyright &y& Elsevier]

When a liquid is cooled below its melting temperature, it usually crystallizes. However, if the quenching rate is fast enough, the system may remain in a disordered state, progressively losing its fluidity upon further cooling. When the time needed for the rearrangement of the local atomic structure reaches approximately 100 seconds, the system becomes "solid" for any practical purpose, and this defines the glass transition temperature T[subg]. Approaching this transition from the liquid side, different systems show qualitatively different temperature dependencies of the viscosity, and accordingly they have been classified by introducing the concept of "fragility." We report experimental observations that relate the microscopic properties of the glassy phase to the fragility. We find that the vibrational properties of the glass well below T[subg] are correlated with the fragility value. Consequently, we extend the fragility concept to the glassy state and indicate how to determine the fragility uniquely from glass properties well below T[subg]. [ABSTRACT FROM AUTHOR]

Numerical studies are providing novel information on the physical processes associated with physical ageing. The process of ageing has been shown to consist of a slow process of explorations of deeper and deeper minima of the system's potential energy surface. In this article we compare the properties of the basins explored in equilibrium with those explored during the ageing process both for sudden temperature changes and for sudden density changes. We find that the hypothesis that during the ageing process the system explores the part of the configuration space explored in equilibrium holds only for shallow quenches or for the early ageing dynamics. At longer times, systematic deviations are observed. In the case of crunches, such deviations are much more apparent. [ABSTRACT FROM AUTHOR]

Acoustic manipulation or perturbation of biological soft matter has emerged as a promising clinical treatment for a number of applications within regenerative medicine, ranging from bone fracture repair to neuromodulation. The potential of ultrasound (US) endures in imparting mechanical stimuli that are able to trigger a cascade of molecular signals within unscathed cells. Particularly, low-intensity pulsed ultrasound (LIPUS) has been associated with bio-effects such as activation of specific cellular pathways and alteration of cell morphology and gene expression, the extent of which can be modulated by fine tuning of LIPUS parameters including intensity, frequency and exposure time. Although the molecular mechanisms underlying LIPUS are not yet fully elucidated, a number of studies clearly define the modulation of specific ultrasonic parameters as a means to guide the differentiation of a specific set of stem cells towards adult and fully differentiated cell types. Herein, we outline the applications of LIPUS in regenerative medicine and the in vivo and in vitro studies that have confirmed the unbounded clinical potential of this platform. We highlight the latest developments aimed at investigating the physical and biological mechanisms of action of LIPUS, outlining the most recent efforts in using this technology to aid tissue engineering strategies for repairing tissue or modelling specific diseases. Ultimately, we detail tissue-specific applications harnessing LIPUS stimuli, offering insights over the engineering of new constructs and therapeutic modalities. Overall, we aim to lay the foundation for a deeper understanding of the mechanisms governing LIPUS-based therapy, to inform the development of safer and more effective tissue regeneration strategies in the field of regenerative medicine. [ABSTRACT FROM AUTHOR]

Exact relation for contributions to heat capacity of liquids is obtained from hydrodynamic theory. It is shown from analysis of the long-wavelength limit of heat density autocorrelation functions that the heat capacity of simple liquids is represented as a sum of two contributions due to 'phonon-like' collective excitations and heat relaxation. The ratio of both contributions being the analogy of Landau-Placzek ratio for heat processes depends on the specific heats ratio. The theory of heat density autocorrelation functions in liquids is verified by computer simulations. Molecular dynamics simulations for six liquids having the ratio of specific heats γ in the range 1.1-2.3, were used for evaluation of the heat density autocorrelation functions and predicted Landau-Placzek ratio for heat processes. The dependence of contributions from collective excitations and heat relaxation process to specific heat on γ is shown to be in excellent agreement with the theory. [ABSTRACT FROM AUTHOR]

We study the instantaneous normal mode (INM) spectrum of a simulated soft-sphere liquid at different equilibrium temperatures T. We find that the spectrum of eigenvalues ρ(λ) has a sharp maximum near (but not at) λ = 0 and decreases monotonically with |λ| on both the stable and unstable sides of the spectrum. The spectral shape strongly depends on temperature. It is rather asymmetric at low temperatures (close to the dynamical critical temperature) and becomes symmetric at high temperatures. To explain these findings we present a mean-field theory for ρ(λ), which is based on a heterogeneous elasticity model, in which the local shear moduli exhibit spatial fluctuations, including negative values. We find good agreement between the simulation data and the model calculations, done with the help of the self-consistent Born approximation (SCBA), when we take the variance of the fluctuations to be proportional to the temperature T. More importantly, we find an empirical correlation of the positions of the maxima of ρ(λ) with the low-frequency exponent of the density of the vibrational modes of the glasses obtained by quenching to T = 0 from the temperature T. We discuss the present findings in connection to the liquid to glass transformation and its precursor phenomena. [ABSTRACT FROM AUTHOR]

Studying the binding processes of G protein-coupled receptors (GPCRs) proteins is of particular interest both to better understand the molecular mechanisms that regulate the signaling between the extracellular and intracellular environment and for drug design purposes. In this study, we propose a new computational approach for the identification of the binding site for a specific ligand on a GPCR. The method is based on the Zernike polynomials and performs the ligand-GPCR association through a shape complementarity analysis of the local molecular surfaces. The method is parameter-free and it can distinguish, working on hundreds of experimentally GPCR-ligand complexes, binding pockets from randomly sampled regions on the receptor surface, obtaining an Area Under ROC curve of 0.77. Given its importance both as a model organism and in terms of applications, we thus investigated the olfactory receptors of the C. elegans, building a list of associations between 21 GPCRs belonging to its olfactory neurons and a set of possible ligands. Thus, we can not only carry out rapid and efficient screenings of drugs proposed for GPCRs, key targets in many pathologies, but also we laid the groundwork for computational mutagenesis processes, aimed at increasing or decreasing the binding affinity between ligands and receptors. [ABSTRACT FROM AUTHOR]

Heterogeneity in the size distribution of cancer cell populations is linked to drug resistance and invasiveness. However, understanding how such heterogeneity arises is still damped by the difficulties of monitoring the proliferation at the typical timescales of mammalian cells. Here, we show how to infer the growth regime and division strategy of leukemia cell populations using live cell fluorescence labeling and flow cytometry in combination with an analytical model where cell growth and division rates depend on powers of the size. We found that the dynamics of the size distribution of Jurkat T-cells is reproduced by (i) a sizer-like division strategy, with (ii) division times following an Erlang distribution and (iii) fluctuations up to ten percent of the inherited fraction of size at division. Overall, our apparatus can be extended to other cell types and environmental conditions allowing for a comprehensive characterization of the growth and division model different cells adopt.Understanding how cancer cells regulate their size is still largely an open question. The authors propose a method to infer the division strategy of leukemia cells via live cell fluorescence labeling and flow cytometry measurements combined with a mathematical model based on size-dependent growth and division rates. [ABSTRACT FROM AUTHOR]

An ideal illumination for light sheet fluorescence microscopy entails both a localized and a propagation invariant optical field. Bessel beams and Airy beams satisfy these conditions, but their non-diffracting feature comes at the cost of the presence of high-energy side lobes that notably degrade the imaging contrast and induce photobleaching. Here, we demonstrate the use of a light droplet illumination whose side lobes are suppressed by interfering Bessel beams of specific k-vectors. Our droplet illumination readily achieves more than 50% extinction of the light distributed across the Bessel side lobes, providing a more efficient energy localization without loss in transverse resolution. In a standard light sheet fluorescence microscope, we demonstrate a two-fold contrast enhancement imaging micron-scale fluorescent beads. Results pave the way to new opportunities for rapid and deep in vivo observations of large-scale biological systems. [ABSTRACT FROM AUTHOR]

We discuss the role of non-hydrodynamic processes in viscoelastic transition in pure liquids. In particular, using both analytical results and molecular dynamics simulations, we clarify the effect of the shear stress relaxation on the transverse dynamics. We use as an example the Lennard-Jones fluids. We analyse the frequency dependence of the shear modulus and its connection to the non-hydrodynamic shear relaxation mode. The analysis of the relaxation times of the non-hydrodynamic modes in longitudinal and transverse dynamics makes evidence that the emergence of the non-hydrodynamic transverse excitations outside the propagation gap is not directly connected to the onset of the positive sound dispersion. [ABSTRACT FROM AUTHOR]

Bioprinting stem cells: building physiological tissues one cell at a time. Am J Physiol Cell Physiol 319: C465-C480, 2020. First published July 8, 2020; doi:10.1152/ajpcell.00124. 2020.--Bioprinting aims to direct the spatial arrangement in three dimensions of cells, biomaterials, and growth factors. The biofabrication of clinically relevant constructs for the repair or modeling of either diseased or damaged tissues is rapidly advancing, resulting in the ability to three-dimensional (3D) print biomimetic platforms which imitate a large number of tissues in the human body. Primary tissue-specific cells are typically isolated from patients and used for the fabrication of 3D models for drug screening or tissue repair purposes. However, the lack of resilience of these platforms, due to the difficulties in harnessing, processing, and implanting patient-specific cells can limit regeneration ability. The printing of stem cells obviates these hurdles, producing functional in vitro models or implantable constructs. Advancements in biomaterial science are helping the development of inks suitable for the encapsulation and the printing of stem cells, promoting their functional growth and differentiation. This review specifically aims to investigate the most recent studies exploring innovative and functional approaches for the printing of 3D constructs to model disease or repair damaged tissues. Key concepts in tissue physiology are highlighted, reporting stem cell applications in biofabrication. Bioprinting technologies and biomaterial inks are listed and analyzed, including recent advancements in biomaterial design for bioprinting applications, commenting on the influence of biomaterial inks on the encapsulated stem cells. Ultimately, most recent successful efforts and clinical potentials for the manufacturing of functional physiological tissue substitutes are reported here, with a major focus on specific tissues, such as vasculature, heart, lung and airways, liver, bone and muscle. [ABSTRACT FROM AUTHOR]

Molecular dynamics (MD) simulations of the glass-former 2Ca(NO3)2·3KNO3, CKN, were performed as a function of temperature at pressures 0.1 MPa, 0.5 GPa, 1.0 GPa, and 2.0 GPa. Diffusion coefficient, relaxation time of the intermediate scattering function, and anion reorientational time were obtained as a function of temperature and densitiy ρ. These dynamical properties of CKN scale as ργ/T with a common value γ = 1.8 ± 0.1. The scaling parameter γ is consistent with the exponent of the repulsive part of an effective intermolecular potential for the repulsion between the atoms at shortest distance in the equilibrium structure of liquid CKN, Ca2+, and oxygen atoms of NO3-. Correlation between potential energy and virial is obeyed for the short-range terms of the potential function, but not for the whole potential including coulombic interactions. Decoupling of diffusion coefficient and reorientational relaxation time from relaxation time take place at a given ργ/T value, i.e., breakdown of Stokes-Einstein and Debye-Stokes-Einstein equations result from combined thermal and volume effects. The MD results agree with correlations proposed between long-time relaxation and short-time dynamics, lnτ ∝ 1/, where the mean square displacement concerns a time window of 10.0 ps. It has been found that scales as ργ/T above and below the glass transition temperature, so that thermodynamic scaling of liquid dynamics can be thought as a consequence of theories relating short- and long-time dynamics, and the more fundamental scaling concerns short-time dynamical properties. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations of the glass-forming liquid 2Ca(NO3)2·3KNO3 (CKN) were performed from high temperature liquid states down to low temperature glassy states at six different pressures from 10-4 to 5.0 GPa. The temperature dependence of the structural relaxation time indicates that the fragility of liquid CKN changes with pressure. In line with recent proposal [Scopigno et al., Science 302, 849 (2003)], the change on liquid fragility is followed by a proportional change of the nonergodicity factor of the corresponding glass at low temperature. [ABSTRACT FROM AUTHOR]

The Hebbian unlearning algorithm, i.e., an unsupervised local procedure used to improve the retrieval properties in Hopfield-like neural networks, is numerically compared to a supervised algorithm to train a linear symmetric perceptron. We analyze the stability of the stored memories: basins of attraction obtained by the Hebbian unlearning technique are found to be comparable in size to those obtained in the symmetric perceptron, while the two algorithms are found to converge in the same region of Gardner's space of interactions, having followed similar learning paths. A geometric interpretation of Hebbian unlearning is proposed to explain its optimal performances. Because the Hopfield model is also a prototypical model of the disordered magnetic system, it might be possible to translate our results to other models of interest for memory storage in materials. [ABSTRACT FROM AUTHOR]

Tauopathies, including Alzheimer's disease and Frontotemporal Dementia, are debilitating neurodegenerative disorders marked by cognitive decline. Despite extensive research, achieving effective treatments and significant symptom management remains challenging. Accurate diagnosis is crucial for developing effective therapeutic strategies, with hyperphosphorylated protein units and tau oligomers serving as reliable biomarkers for these conditions. This study introduces a novel approach using nanotechnology to enhance the diagnostic process for tauopathies. We developed humanized ferritin nanocages, a novel nanoscale delivery system, designed to encapsulate and transport a tau-specific fluorophore, BT1, into human retinal cells for detecting neurofibrillary tangles in retinal tissue, a key marker of tauopathies. The delivery of BT1 into living cells was successfully achieved through these nanocages, demonstrating efficient encapsulation and delivery into retinal cells derived from human induced pluripotent stem cells. Our experiments confirmed the colocalization of BT1 with pathological forms of tau in living retinal cells, highlighting the method's potential in identifying tauopathies. Using ferritin nanocages for BT1 delivery represents a significant contribution to nanobiotechnology, particularly in neurodegenerative disease diagnostics. This method offers a promising tool for the early detection of tau tangles in retinal tissue, with significant implications for improving the diagnosis and management of tauopathies. This study exemplifies the integration of nanotechnology with biomedical science, expanding the frontiers of nanomedicine and diagnostic techniques. [ABSTRACT FROM AUTHOR]

The nematode Caenorhabditis elegans is a widely used model organism for neuroscience. Although its nervous system has been fully reconstructed, the physiological bases of single-neuron functioning are still poorly explored. Recently, many efforts have been dedicated to measuring signals from C. elegans neurons, revealing a rich repertoire of dynamics, including bistable responses, graded responses, and action potentials. Still, biophysical models able to reproduce such a broad range of electrical responses lack. Realistic electrophysiological descriptions started to be developed only recently, merging gene expression data with electrophysiological recordings, but with a large variety of cells yet to be modeled. In this work, we contribute to filling this gap by providing biophysically accurate models of six classes of C. elegans neurons, the AIY, RIM, and AVA interneurons, and the VA, VB, and VD motor neurons. We test our models by comparing computational and experimental time series and simulate knockout neurons, to identify the biophysical mechanisms at the basis of inter and motor neuron functioning. Our models represent a step forward toward the modeling of C. elegans neuronal networks and virtual experiments on the nematode nervous system. [ABSTRACT FROM AUTHOR]

The article highlights the study by Hiroshi Shintani and Hajime Tanaka, published within the issue, which looks at the origin of the boson peak, the universal features of the anomalous properties of amorphous solids such as glasses. It mentions that the boson peak, is shown to be directly linked to transverse vibrations in the phonon spectrum.

The architecture of communication within the brain, represented by the human connectome, has gained a paramount role in the neuroscience community. Several features of this communication, e.g. , the frequency content, spatial topology, and temporal dynamics are currently well established. However, identifying generative models providing the underlying patterns of inhibition/excitation is very challenging. To address this issue, we present a novel generative model to estimate large-scale effective connectivity from MEG. The dynamic evolution of this model is determined by a recurrent Hopfield neural network with asymmetric connections, and thus denoted Recurrent Hopfield Mass Model (RHoMM). Since RHoMM must be applied to binary neurons, it is suitable for analyzing Band Limited Power (BLP) dynamics following a binarization process. We trained RHoMM to predict the MEG dynamics through a gradient descent minimization and we validated it in two steps. First, we showed a significant agreement between the similarity of the effective connectivity patterns and that of the interregional BLP correlation, demonstrating RHoMM's ability to capture individual variability of BLP dynamics. Second, we showed that the simulated BLP correlation connectomes, obtained from RHoMM evolutions of BLP, preserved some important topological features, e.g , the centrality of the real data, assuring the reliability of RHoMM. Compared to other biophysical models, RHoMM is based on recurrent Hopfield neural networks, thus, it has the advantage of being data-driven, less demanding in terms of hyperparameters and scalable to encompass large-scale system interactions. These features are promising for investigating the dynamics of inhibition/excitation at different spatial scales. • A novel generative model (RHoMM) can predict the dynamics of MEG/EEG time-series. • RHoMM is based on a recurrent Hopfield neural network, connecting brain regions. • RHoMM is data-driven, uses a few hyperparameters, and can be easily scaled. • The functional architecture generated by RHoMM's reproduces the experimental data. [ABSTRACT FROM AUTHOR]

The object of this study was the recognition of Regions Of Interest(ROIs) in a time series of digital images of two specific laboratory experiments. It concerns the identification of objects in a tissue surface by high-resolution and high-speed ad-hoc systems for morphological dynamic image analysis. The protocols and the algorithms implemented are developed to retrieve biomechanical properties of two different in vitro systems; the solid filament X-MET (eX-vivo Muscle Engineered Tissue) to measure its reaction to a different frequency stimulation, and a planar system of co-culture of skeletal and cardiac muscle cells, where myotubes and cardiomyocytes coexist, to discriminate the interaction between different cell's type, of its spontaneous pulse. The results of the stimulated X-MET from solid culture system are frequency dependent points of the macroscopic muscular strength and its contractile response. The results for the co-culture planar board measure the correlation of the pulsed movements of the different parts of the tissue. [ABSTRACT FROM AUTHOR]

In optics, Bessel beams have seen extensive use because they exhibit a non-diffracting propagation and a self-reconstruction capability beyond obstacles encountered along their path, with an ensuing pronounced resilience to scattering. Whether such peculiarities, characteristic of the Helmholtz equation for transverse E and B fields, are manifested by longitudinal acoustic fields is currently unknown. Here, we report the experimental demonstration of the self-healing and the scattering resilience properties of a non-diffracting zero-order acoustic Bessel beam. The beam is obtained interfering ultrasound waves with a propagating vector lying on a cone and is found to be capable of self-reconstructing beyond large spherical obstacles and multiple scattering layers. [ABSTRACT FROM AUTHOR]

An effective fitting scheme within the thermo-viscoelastic model is proposed for estimation of dynamic eigenmodes of an ionic melt from ab initio molecular dynamics (AIMD) simulations. Dynamic eigenmodes are solutions of the generalized Langevin equation in matrix form, obtained on the basis set of eight dynamic variables. Fitting parameters are used only in the generalized hydrodynamic matrix T (k) for matrix elements involving heat density and heat current correlations only, because of huge computational efforts needed to calculate them directly in ab initio simulations. In the proposed scheme six AIMD-derived time correlation functions, three partial density-density and three partial current-current ones, are recovered by the proposed theoretical approach, which satisfies the exact sum rules up to the fourth frequency moments of partial dynamic structure factors. The suggested theoretical analysis was applied to estimation of propagating hydrodynamic and non-hydrodynamic eigenmodes in molten NaCl. • A new ab initio methodology of analysis of collective dynamics in binary liquids and ionic liquids. • Calculations by a combination of ab initio simulations and GCM theory of collective excitations in liquids. • Dispersions of acoustic and optic eigenmodes in molten NaCl obtained by the new methodology. • Molten NaCl is known for experimental observation of non-hydrodynamic optic modes. [ABSTRACT FROM AUTHOR]

The time evolution of both dynamic and static structure factors of a charged colloidal clay, Laponite, dispersed in both H2O and D2O solvents has been investigated through multiangle dynamic light scattering (DLS) and small-angle X-ray scattering (SAXS) as a function of weight concentration. The aging phenomenology and the formation of arrested states, both gel and glass, are preserved in D2O, while the dynamics is slowed down with respect to water. These findings are important to understand the role played by the solvent in the interparticle interactions and for techniques such as neutron scattering and nuclear magnetic resonance that allow for the extension of the accessible scattering vectors and time scales. [ABSTRACT FROM AUTHOR]

Flow cytometers and fluorescence activated cells sorters (FCM/FACS) represent the gold standard for high-throughput single-cell analysis, but their usefulness for label-free applications is limited by the unreliability of forward and side scatter measurements. Scanning flow cytometers represent an appealing alternative, as they exploit measurements of the angle-resolved scattered light to provide accurate and quantitative estimates of cellular properties, but the requirements of current setups are unsuitable for integration with other lab-on-chip technologies or for point-of-care applications. Here we present the first microfluidic scanning flow cytometer (μSFC), able to achieve accurate angle-resolved scattering measurements within a standard polydimethylsiloxane microfluidic chip. The system exploits a low cost linearly variable optical density (OD) filter to reduce the dynamic range of the signal and to increase its signal-to-noise ratio. We present a performance comparison between the μSFC and commercial machines for the label free characterization of polymeric beads with different diameters and refractive indices. In contrast to FCM and FACS, the μSFC yields size estimates linearly correlated with nominal particle sizes (R2 = 0.99) and quantitative estimates of particle refractive indices. The feasibility of using the μSFC for the characterization of biological samples is demonstrated by analyzing a population of monocytes identified based on the morphology of a peripheral blood mononuclear cells sample, which yields values in agreement with the literature. The proposed μSFC combines low setup requirements with high performance, and has great potential for integration within other lab-on-chip systems for multi-parametric cell analysis and for next-generation point-of-care diagnostic applications. [ABSTRACT FROM AUTHOR]

In the last decade, 3D printing systems have greatly evolved both in terms of processable materials and printing resolutions, becoming a top seed technology for many academic and industrial applications. Nevertheless, manufacturing polymeric materials characterized by a trabecular porosity and functionally graded architecture—where both the local porosity and chemical composition of the matrix change in the 3D space—through additive platforms remains an open technical challenge. In this study, a 3D extrusion printing strategy to tackle this problem is presented. The proposed systems are based on a flow‐focusing microfluidic printing head—to continuously generate oil‐in‐water emulsion inks—and on an agarose fluid–gel used as a temporary support bath for the deposition of the photo‐curable emulsion inks. It is demonstrated that through this strategy one can design a priori and build with high accuracy both discontinuous and continuous functionally graded polymeric foams, where both the density and composition of the materials could be varied independently within arbitrarily complex 3D architectures. This study provides new means for the synthesis of microporous, polymeric FGMs which could find applications ranging from interface tissue engineering to automotive and construction industries. [ABSTRACT FROM AUTHOR]

The theory of elasticity with spatially fluctuating elastic constants (heterogeneous-elasticity theory) is reviewed. It is shown that the vibrational anomalies associated with the boson peak can be qualitatively and quantitatively explained in terms of this theory. Two versions of a mean-field theory for solving the stochastic equation of motion are presented: the coherent-potential approximation (CPA) and the self-consistent Born approximation (SCBA). It is shown that the latter is included in the former in the Gaussian and weak-disorder limit. We are able to discuss and explain cases in which the change of the vibrational spectrum by varying an external parameter can be accounted for by changing the Debye frequency (elastic transformation) and cases in which this is not possible. In the latter case a change in the distribution of the elastic moduli has occurred. [ABSTRACT FROM AUTHOR]

Static and dynamic autocorrelations of charge density, composed of positive point ions and instantaneous distribution of electron density, are studied in liquid Li in a pressure range from ambient to 186 GPa using ab initio molecular dynamics simulations. It is shown analytically that the long-wavelength limit of the charge-charge static structure factor SQQ (k) of liquid metals is proportional to k4. Time-dependent charge-charge correlations in liquid Li at low pressures show identical relaxation as the density-density time correlation functions, in complete agreement with the linear response theory, whereas at extreme pressures we observed different relaxation of the charge and density autocorrelations. The static and dynamic properties of a part of electron density, that corresponds to the nonspherical distribution around ions, are discussed. [ABSTRACT FROM AUTHOR]

What are the molecular determinants of protein–protein binding affinity and whether they are similar to those regulating fold stability are two major questions of molecular biology, whose answers bring important implications both from a theoretical and applicative point of view. Here, we analyze chemical and physical features on a large dataset of protein–protein complexes with reliable experimental binding affinity data and compare them with a set of monomeric proteins for which melting temperature data was available. In particular, we probed the spatial organization of protein (1) intramolecular and intermolecular interaction energies among residues, (2) amino acidic composition, and (3) their hydropathy features. Analyzing the interaction energies, we found that strong Coulombic interactions are preferentially associated with a high protein thermal stability, while strong intermolecular van der Waals energies correlate with stronger protein–protein binding affinity. Statistical analysis of amino acids abundances, exposed to the molecular surface and/or in interaction with the molecular partner, confirmed that hydrophobic residues present on the protein surfaces are preferentially located in the binding regions, while charged residues behave oppositely. Leveraging on the important role of van der Waals interface interactions in binding affinity, we focused on the molecular surfaces in the binding regions and evaluated their shape complementarity, decomposing the molecular patches in the 2D Zernike basis. For the first time, we quantified the correlation between local shape complementarity and binding affinity via the Zernike formalism. In addition, considering the solvent interactions via the residue hydropathy, we found that the hydrophobicity of the binding regions dictates their shape complementary as much as the correlation between van der Waals energy and binding affinity. In turn, these relationships pave the way to the fast and accurate prediction and design of optimal binding regions as the 2D Zernike formalism allows a rapid and superposition-free comparison between possible binding surfaces. [ABSTRACT FROM AUTHOR]

In this study, transmission electron microscopy atomic force microscopy, and surface enhanced Raman spectroscopy are combined through a direct imaging approach, to gather structural and chemical information of complex molecular systems such as ion channels in their original plasma membrane. Customized microfabricated sample holder allows to characterize Nav channels embedded in the original plasma membrane extracted from neuronal cells that are derived from healthy human induced pluripotent stem cells. The identification of the channels is accomplished by using two different approaches, one of them widely used in cryo‐EM (the particle analysis method) and the other based on a novel Zernike Polynomial expansion of the images bitmap. This approach allows to carry out a whole series of investigations, one complementary to the other, on the same sample, preserving its state as close as possible to the original membrane configuration. [ABSTRACT FROM AUTHOR]

The spatial fluctuations of the dynamics of a colloidal system composed of nanoparticles are probed by a novel experimental setup, which combines homodyne and heterodyne dynamic light scattering focused onto a micron-sized volume via a microscope objective. The technique is used to measure the four-point susceptibility of an aging colloidal suspension, revealing a breakdown of the Gaussian approximation for the correlation function of the scattered electromagnetic field. The deviation from the Gaussian approximation increases with waiting time as the system evolves toward an arrested phase, signaling the gradual emergence of higher-order nontrivial dynamic correlations. [ABSTRACT FROM AUTHOR]

Blind-structured illumination microscopy (blind-SIM) enhances the optical resolution without the requirement of nonlinear effects or pre-defined illumination patterns. It is thus advantageous in experimental conditions where toxicity or biological fluctuations are an issue. In this work, we introduce a custom convolutional neural network architecture for blind-SIM: BS-CNN. We show that BS-CNN outperforms other blind-SIM deconvolution algorithms providing a resolution improvement of 2.17 together with a very high Fidelity (artifacts reduction). Furthermore, BS-CNN proves to be robust in cross-database variability: it is trained on synthetically augmented open-source data and evaluated on experiments. This approach paves the way to the employment of CNN-based deconvolution in all scenarios in which a statistical model for the illumination is available while the specific realizations are unknown or noisy. [ABSTRACT FROM AUTHOR]

The present investigation focuses on the analysis of the interactions among human lactoferrin (LF), SARS-CoV-2 receptor-binding domain (RBD) and human angiotensin-converting enzyme 2 (ACE2) receptor in order to assess possible mutual interactions that could provide a molecular basis of the reported preventative effect of lactoferrin against CoV-2 infection. In particular, kinetic and thermodynamic parameters for the pairwise interactions among the three proteins were measured via two independent techniques, biolayer interferometry and latex nanoparticle-enhanced turbidimetry. The results obtained clearly indicate that LF is able to bind the ACE2 receptor ectodomain with significantly high affinity, whereas no binding to the RBD was observed up to the maximum "physiological" lactoferrin concentration range. Lactoferrin, above 1 µM concentration, thus appears to directly interfere with RBD–ACE2 binding, bringing about a measurable, up to 300-fold increase of the KD value relative to RBD–ACE2 complex formation. [ABSTRACT FROM AUTHOR]

Most proteins perform their biological function by interacting with one or more molecular partners. In this respect, characterizing local features of the molecular surface, that can potentially be involved in the interaction with other molecules, represents a step forward in the investigation of the mechanisms of recognition and binding between molecules. Predictive methods often rely on extensive samplings of molecular patches with the aim to identify hot spots on the surface. In this framework, analysis of large proteins and/or many molecular dynamics frames is often unfeasible due to the high computational cost. Thus, finding optimal ways to reduce the number of points to be sampled maintaining the biological information (including the surface shape) carried by the molecular surface is pivotal. In this perspective, we here present a new theoretical and computational algorithm with the aim of defining a set of molecular surfaces composed of points not uniformly distributed in space, in such a way as to maximize the information of the overall shape of the molecule by minimizing the number of total points. We test our procedure's ability in recognizing hot-spots by describing the local shape properties of portions of molecular surfaces through a recently developed method based on the formalism of 2D Zernike polynomials. The results of this work show the ability of the proposed algorithm to preserve the key information of the molecular surface using a reduced number of points compared to the complete surface, where all points of the surface are used for the description. In fact, the methodology shows a significant gain of the information stored in the sampling procedure compared to uniform random sampling. [ABSTRACT FROM AUTHOR]

Numerous studies have shown a strong correlation between the number of neurofibrillary tangles of the tau protein and Alzheimer's disease progression, making the quantitative detection of tau very promising from a clinical point of view. However, the lack of highly reliable fluorescent probes for selective imaging of tau neurofibrillary tangles is a major challenge due to sharing similar β–sheet motifs with homologous Amyloid-β fibrils. In the current work, we describe the rational design and the in silico evaluation of a small-size focused library of fluorescent probes, consisting of a BODIPY core (electron acceptor) featuring highly conjugated systems (electron donor) with a length in the range 13–19 Å at C3. Among the most promising probes in terms of binding mode, theoretical affinity and polarity, BT1 has been synthesized and tested in vitro onto human induced pluripotent stem cells derived neuronal cell cultures. The probe showed excellent photophysical properties and high selectivity allowing in vitro imaging of hyperphosphorylated tau protein filaments with minimal background noise. Our findings offer new insight into the structure-activity relationship of this class of tau selective fluorophores, paving the way for boosting tau tangle detection in patients possibly through retinal spectral scans. [ABSTRACT FROM AUTHOR]