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Renal Cell Carcinoma is typically asymptomatic at the early stages for many patients. This leads to a late diagnosis of the tumor, where the curability likelihood is lower, and makes the mortality rate of Renal Cell Carcinoma high, with respect to its incidence rate. To increase the survival chance, a fast and correct categorization of the tumor subtype is paramount. Nowadays, computerized methods, based on artificial intelligence, represent an interesting opportunity to improve the productivity and the objectivity of the microscopy-based Renal Cell Carcinoma diagnosis. Nonetheless, much of their exploitation is hampered by the paucity of annotated dataset, essential for a proficient training of supervised machine learning technologies. This study sets out to investigate a novel self supervised training strategy for machine learning diagnostic tools, based on the multi-resolution nature of the histological samples. We aim at reducing the need of annotated dataset, without significantly reducing the accuracy of the tool. We demonstrate the classification capability of our tool on a whole slide imaging dataset for Renal Cancer subtyping, and we compare our solution with several state-of-the-art classification counterparts.

Recently we investigated from first principles screening properties in systems where small molecules, characterized by a finite electronic dipole moment, are encapsulated into different nanocages. The most relevant result was the observation of an antiscreening effect in alkali-halide nanocages characterized by ionic bonds. Here we extend the study to another class of nanostructures, the nanotubes. Using first-principles techniques based on the Density Functional Theory, we studied the properties of endohedral nanotubes obtained by encapsulation of a water molecule or a linear HF molecule. A detailed analysis of the effective dipole moment of the complexes and of the electronic charge distribution suggests that screening effects crucially depend not only on the nature of the intramolecular bonds but also on the size and the shape of the nanotubes, and on the specific encapsulated molecule. As observed in endohedral nanocages, screening is maximum in covalent-bond carbon nanotubes, while it is reduced in partially-ionic nanotubes and an antiscreening effect is observed in some ionic nanotubes. However in this case the scenario is more complex than in corresponding ionic nanocages. In fact the specific geometric structure of alkali-halide nanotubes turns out to be crucial for determining the screening/antiscreening behavior: while nanotubes with octagonal transversal section can exhibit an antiscreening effect, which quantitatively depends on the number of layers in the longitudinal direction, instead nanotubes with dodecagonal section are always characterized by a reduction of the total dipole moment, so that a screening behavior is observed. Our results therefore show that, even in nanotube structures, in principle one can tune the dipole moment and generate electrostatic fields at the nanoscale without the aid of external potentials., Comment: 11 figures. arXiv admin note: text overlap with arXiv:2210.05324

Superfluidity is a well-characterized quantum phenomenon which entails frictionless-motion of mesoscopic particles through a superfluid, such as $^4$He or dilute atomic-gases at very low temperatures. As shown by Landau, the incompatibility between energy- and momentum-conservation, which ultimately stems from the spectrum of the elementary excitations of the superfluid, forbids quantum-scattering between the superfluid and the moving mesoscopic particle, below a critical speed-threshold. Here we predict that frictionless-motion can also occur in the absence of a standard superfluid, i.e. when a He atom travels through a narrow (5,5) carbon-nanotube (CNT). Due to the quasi-linear dispersion of the plasmon and phonon modes that could interact with He, the (5,5) CNT embodies a solid-state analog of the superfluid, thereby enabling straightforward transfer of Landau's criterion of superfluidity. As a result, Landau's equations acquire broader generality, and may be applicable to other nanoscale friction phenomena, whose description has been so far purely classical.

We investigate from first principles screening effects in endohedral complexes when small molecules, characterized by a finite electronic dipole moment, such as HF, LiF, NaCl, and H$_2$O, are encapsulated into different nanoscale cages. We find that screening effects crucially depend on the nature of the intramolecular bonds of the cage: screening is maximum in covalent-bond carbon nanocages, while it is reduced in partially-ionic ones. Interestingly, in the case of the ionic-bond nanocages, an antiscreening effect is observed: due to the relative displacement of positive and negative ions, induced by the dipole moment of the encapsulated molecule, these cages act as dipole-field amplifiers. Our results open the way to the possibility of tuning the dipole moment of nanocages and of generating electrostatic fields at the nanoscale without the aid of external potentials. Moreover, we can expect some transferability of the observed screening effects also to nanotubes and 2D materials.

Water-flow in carbon nanotubes (CNT's) starkly contradicts classical fluid mechanics, with permeabilities that can exceed no-slip Haagen-Poiseuille predictions by two to five orders of magnitude. Semi-classical molecular dynamics accounts for enhanced flow-rates, that are attributed to curvature-dependent lattice mismatch. However, the steeper permeability-enhancement observed experimentally at $\sim$nm-size radii remains poorly understood, and suggests emergence of puzzling non-classical mechanisms. Here we address water-CNT friction from a quantum-mechanical perspective, in terms of water-energy loss upon phonon excitation. We find that combined weak water-phonon coupling and selection rules hinder water-CNT scattering, providing effective protection to water superflow, whereas comparison with a semiclassical theory evidences a friction increase that can exceed the quantum-mechanical prediction by more than two orders of magnitude. Quasi-frictionless flow up to sub-nm CNT's opens new pathways towards minimally-invasive trans-membrane cellular injections, single-water fluidics and efficient water filtration.

Understanding static and dynamic phenomena in complex materials at different length scales requires reliably accounting for van der Waals (vdW) interactions, which stem from long-range electronic correlations. While the important role of many-body vdW interactions has been extensively documented when it comes to the stability of materials, much less is known about the coupling between vdW interactions and atomic forces. Here we analyze the Hessian force response matrix for a single and two vdW-coupled atomic chains to show that a many-body description of vdW interactions yields atomic force response magnitudes that exceed the expected pairwise decay by 3-5 orders of magnitude for a wide range of separations between the perturbed and the observed atom. Similar findings are confirmed for graphene and carbon nanotubes. This colossal force enhancement suggests implications for phonon spectra, free energies, interfacial adhesion, and collective dynamics in materials with many interacting atoms.

We investigate energetic and electronic properties of TiS2 , an archetypal van der Waals (vdW) material, from first principles, in the framework of the Density Functional Theory (DFT). In this system a recent experimental study showed a puzzling discrepancy between the distribution of the electron density in the interlayer region obtained by X-ray diffraction data and that computed by DFT, even adopting DFT functionals that should properly include vdW effects. Such a discrepancy could indicate a partial failure of state-of-the-art DFT approaches in describing the weak interlayer interactions of TiS2 and, possibly, of similar systems too. In order to shed light on this issue, we have carried out simulations based on different DFT functionals, basically confirming the mentioned discrepancy with the experimental findings. Subsequently, we have tried to reproduce the experimental interlayer electronic density deformation both by changing the parameters characterizing the rVV10 DFT functional (in such a way to artificially modify the strength of the vdW interactions at short or long range), and also by adopting a modified pseudopotential for Sulfur atoms, involving d orbitals. The latter approach turns out to be particularly promising. In fact, using this novel, more flexible pseudopotential, we obtain not only an electronic density deformation closer to the experimental profile, but also a better estimate of the interlayer binding energy. Interestingly, this improvement in the theoretical DFT description is not limited to TiS2 but also applies to other similar layered systems involving S atoms, such as TaS2 , HfS2 , and MoS2 ., Comment: Main text: 26 Pages. Sppelementary informations: 4 Pages. Eight Figures, eight Tables. To be published in Journal of Physical Chemistry C (JPC C)

In the recent years, therapeutic use of antibodies has seen a huge growth, due to their inherent proprieties and technological advances in the methods used to study and characterize them. Effective design and engineering of antibodies for therapeutic purposes are heavily dependent on knowledge of the structural principles that regulate antibody-antigen interactions. Several experimental techniques such as X-ray crystallography, cryo-electron microscopy, NMR or mutagenesis analysis can be applied, but these are usually expensive and time consuming. Therefore computational approaches like molecular docking may offer a valuable alternative for the characterisation of antibody-antigen complexes. Here we describe a protocol for the prediction of the 3D structure of antibody-antigen complexes using the integrative modelling platform HADDOCK. The protocol consists of: 1) The identification of the antibody residues belonging to the hyper variable loops which are known to be crucial for the binding and can be used to guide the docking; 2) The detailed steps to perform docking with the HADDOCK 2.4 webserver following different strategies depending on the availability of information about epitope residues., Comment: 22 pages, 4 figures

Traditional simulations on High-Performance Computing (HPC) systems typically involve modeling very large domains and/or very complex equations. HPC systems allow running large models, but limits in performance increase that have become more prominent in the last 5-10 years will likely be experienced. Therefore new approaches are needed to increase application performance. Deep learning appears to be a promising way to achieve this. Recently deep learning has been employed to enhance solving problems that traditionally are solved with large-scale numerical simulations using HPC. This type of application, deep learning for high-performance computing, is the theme of this whitepaper. Our goal is to provide concrete guidelines to scientists and others that would like to explore opportunities for applying deep learning approaches in their own large-scale numerical simulations. These guidelines have been extracted from a number of experiments that have been undertaken in various scientific domains over the last two years, and which are described in more detail in the Appendix. Additionally, we share the most important lessons that we have learned., Comment: White paper consists of 36 pages and 15 figures

The fully polarizable QM/MM approach based on fluctuating charges and fluctuating dipoles, named QM/FQF{\mu} (J. Chem. Theory Comput. 2019, 15, 2233-2245), is extended to the evaluation of nuclear gradients and the calculation of IR spectra of molecular systems in condensed phase. To this end, analytical equations defining first and second energy derivatives with respect to nuclear coordinates are derived and discussed. The potentialities of the approach are shown by applying the model to the calculation of IR spectra of Methlyoxirane, Glycidol and Gallic Acid in aqueous solution. The results are compared with the continuum QM/PCM and the polarizable QM/FQ, which is based on Fluctuating Charges only., Comment: 42 pages, 11 figures

Fully polarizable QM/MM approach based on fluctuating charges and fluctuating dipoles, named QM/FQF{\mu} (J. Chem. Theory Comput. 2019, 15 2233-2245), is extended to the calculation of vertical excitation energies of solvated molecular systems. Excitation energies are defined within two different solvation regimes, i.e. linear response (LR), where the response of the MM portion is adjusted to the QM transition density, and corrected-Linear Response (cLR) in which the MM response is adjusted to the relaxed QM density, thus being able to account for charge equilibration in the excited state. The model, which is specified in terms of three physical parameters (electronegativity, chemical hardness, and polarizability) is applied to vacuo-to-water solvatochromic shifts of aqueous solutions of para-nitroaniline, pyridine and pyrimidine. The results show a good agreement with their experimental counterparts, thus highlighting the potentialities of this approach., Comment: 14 pages, 8 figures

We present the extension of the quantum/classical polarizable fluctuating charge model to the calculation of single residues of quadratic response functions, as required for the computational modeling of two-photon absorption cross-sections. By virtue of a variational formulation of the quantum/classical polarizable coupling, we are able to exploit an atomic orbital-based quasienergy formalism to derive the additional coupling terms in the response equations. Our formalism can be extended to the calculation of arbitrary order response functions and their residues. The approach has been applied to the challenging problem of one- and two-photon spectra of rhodamine 6G (R6G) in aqueous solution. Solvent effects on one- and two-photon spectra of R6G in aqueous solution have been analyzed by considering three different approaches, from a continuum (QM/PCM) to two QM/MM models (non-polarizable QM/TIP3P and polarizable QM/FQ). Both QM/TIP3P and QM/FQ simulated OPA and TPA spectra show that the inclusion of discrete water solvent molecules is essential to increase the agreement between theory and experiment. QM/FQ has been shown to give the best agreement with experiments.

A new implementation is proposed for including van der Waals (vdW) interactions in Density Functional Theory (DFT) using the Maximally-Localized Wannier functions (MLWFs), which is free from empirical parameters. With respect to the previous DFT/vdW-WF2 method, in the present DFT/vdW-WF2-x approach, the empirical, short-range, damping function is replaced by an estimate of the Pauli exchange repulsion, also obtained by the MLWFs properties. Applications to systems contained in the popular S22 molecular database and to the case of an Ar atom interacting with graphite, and comparison with reference data, indicate that the new method, besides being more physically founded, also leads to a systematic improvement in the description of vdW-bonded systems., Comment: 3 figures. arXiv admin note: text overlap with arXiv:1111.6737, arXiv:1305.7035, arXiv:1603.08667

Recent atomic force microscopy (AFM) experiments~[ACS Nano {\bf 2014}, 8, 12410-12417] conducted on graphene-coated SiO$_2$ demonstrated that monolayer graphene (G) can effectively screen dispersion van der Waals (vdW) interactions deriving from the underlying substrate: despite the single-atom thickness of G, the AFM tip was almost insensitive to SiO$_2$, and the tip-substrate attraction was essentially determined only by G. This G vdW {\it opacity} has far reaching implications, encompassing stabilization of multilayer heterostructures, micromechanical phenomena or even heterogeneous catalysis. Yet, detailed experimental control and high-end applications of this phenomenon await sound physical understanding of the underlying physical mechanism. By quantum many-body analysis and ab-initio Density Functional Theory, here we address this challenge providing theoretical rationalization of the observed G vdW {\it opacity} for weakly interacting substrates. The non-local density response and ultra slow decay of the G vdW interaction ensure compensation between standard attractive terms and many-body repulsive contributions, enabling vdW {\it opacity} over a broad range of adsorption distances. vdW {\it opacity} appears most efficient in the low frequency limit and extends beyond London dispersion including electrostatic Debye forces. By virtue of combined theoretical/experimental validation, G hence emerges as a promising ultrathin {\it shield} for modulation and switching of vdW interactions at interfaces and complex nanoscale devices.

The Lifshitz-Zaremba-Kohn (LZK) theory is commonly considered as the correct large-distance limit for the van der Waals (vdW) interaction of adsorbates (atoms, molecules, or nanoparticles) with solid substrates. In the standard approximate form, implicitly based on "local" dielectric functions, the LZK approach predicts universal power laws for vdW interactions depending only on the dimensionality of the interacting objects. However, recent experimental findings are challenging the universality of this theoretical approach at finite distances of relevance for nanoscale assembly. Here, we present a combined analytical and numerical many-body study demonstrating that physical adsorption can be significantly enhanced at the nanoscale. Regardless of the band gap or the nature of the adsorbate specie, we find deviations from conventional LZK power laws that extend to separation distances of up to 10--20 nanometers. Comparison with recent experimental observation of ultra long-ranged vdW interactions in the delamination of graphene from a silicon substrate reveals qualitative agreement with the present theory. The sensitivity of vdW interactions to the substrate response and to the adsorbate characteristic excitation frequency also suggests that adsorption strength can be effectively tuned in experiments, paving the way to an improved control of physical adsorption at the nanoscale.

Working with a gauge coupling field in a linear superfield, we construct effective Lagrangians for N=1 super-Yang-Mills theory fully compatible with the expected all-order behaviour or physical quantities. Using the one-loop dependence on its ultraviolet cutoff and anomaly matching or cancellation of R and dilatation anomalies, we obtain the Wilsonian effective Lagrangian. With similar anomaly matching or cancellation methods, we derive the effective action for gaugino condensates, as a function of the real coupling field. Both effective actions lead to a derivation of the NSVZ beta function from algebraic arguments only. The extension of results to N=2 theories or to matter systems is briefly considered. The main tool for the discussion of anomalies is a generic supercurrent structure with 16_B+16_F operators (the S multiplet), which we derive using superspace identities and field equations for a fully general gauge theory Lagrangian with the linear gauge coupling superfield, and with various U(1)_R currents. As a byproduct, we show under which conditions the S multiplet can be improved to contain the Callan-Coleman-Jackiw energy-momentum tensor whose trace measures the breaking of scale invariance., Comment: 60 pages, references added, published version (Nucl. Phys. B)

Due to the recent experimental progress, tunable spin-orbit (SO) interactions represent ideal candidates for the control of polarization and dynamical spin properties in both quantum wells and cold atomic systems. A detailed understanding of spin properties in SO coupled systems is thus a compelling prerequisite for possible novel applications or improvements in the context of spintronics and quantum computers. Here we analyze the case of equal Rashba and Dresselhaus couplings in both homogeneous and laterally confined two-dimensional systems. Starting from the single-particle picture and subsequently introducing two-body interactions we observe that periodic spin fluctuations can be induced and maintained in the system. Through an analytical derivation we show that the two-body interaction does not involve decoherence effects in the bosonic dimer, and, in the repulsive homogeneous Fermi gas it may be even exploited in combination with the SO coupling to induce and tune standing currents. By further studying the effects of a harmonic lateral confinement --a particularly interesting case for Bose condensates-- we evidence the possible appearance of non-trivial {\it spin textures}, whereas the further application of a small Zeeman-type interaction can be exploited to fine-tune the system polarizability., Comment: 13 pages, 3 figures

The cohesive energy, equilibrium lattice constant, and bulk modulus of noble metals are computed by different van der Waals-corrected Density Functional Theory methods, including vdW-DF, vdW-DF2, vdW-DF-cx, rVV10 and PBE-D. Two specifically-designed methods are also developed in order to effectively include dynamical screening effects: the DFT/vdW-WF2p method, based on the generation of Maximally Localized Wannier Functions, and the RPAp scheme (in two variants), based on a single-oscillator model of the localized electron response. Comparison with results obtained without explicit inclusion of van der Waals effects, such as with the LDA, PBE, PBEsol, or the hybrid PBE0 functional, elucidates the importance of a suitable description of screened van der Waals interactions even in the case of strong metal bonding. Many-body effects are also quantitatively evaluated within the RPAp approach., Comment: 3 figures

The DFT/vdW-WF2s1 method based on the generation of localized Wannier functions, recently developed to include the van der Waals interactions in the Density Functional Theory and describe adsorption processes on metal surfaces by taking metal-screening effects into account, is applied to the case of the interaction of Xe with noble-metal surfaces, namely Ag(111), Au(111), and Cu(111). The study is also repeated by adopting the DFT/vdW-QHO-WF variant relying on the Quantum Harmonic Oscillator model which describes well many-body effects. Comparison of the computed equilibrium binding energies and distances, and the $C_3$ coefficients characterizing the adatom-surface van der Waals interactions, with available experimental and theoretical reference data shows that the methods perform well and elucidate the importance of properly including screening effects. The results are also compared with those obtained by other vdW-corrected DFT schemes, including PBE-D, vdW-DF, vdW-DF2, rVV10, and by the simpler Local Density Approximation (LDA) and semilocal (PBE) Generalized Gradient Approximation (GGA) approaches., Comment: 1 figure

We develop generalization of the fixed-phase diffusion Monte Carlo method for Hamiltonians which explicitly depend on particle spins such as for spin-orbit interactions. The method is formulated in zero variance manner and is similar to treatment of nonlocal operators in commonly used static- spin calculations. Tests on atomic and molecular systems show that it is very accurate, on par with the fixed-node method. This opens electronic structure quantum Monte Carlo methods to a vast research area of quantum phenomena in which spin-related interactions play an important role., Comment: Version 3: Some text additions. Results and conclusions unchanged. 5 pages, 2 figures

The DFT/vdW-WF2s1 method, recently developed to include the van der Waals interactions in the Density Functional Theory and describe adsorption processes on metal surfaces by taking metal-screening effects into account, is applied to the case of the interaction of Xe and graphene with a transition-metal surface, namely Ni(111). In general the adsorption of rare-gas atoms on metal surfaces is important because is prototypical for physisorption processes. Moreover, the interaction of graphene with Ni(111) is of particular interest for practical applications (efficient and large-scale production of high-quality graphene) and, from a theoretical point of view, is particularly challenging, since it can be described by a delicate interplay between chemisorption and physisorption processes. The first-principles simulation of transition metals require particular care also because they can be viewed as intermediate systems between simple metals and insulating crystals. Even in these cases the method performs well as demonstrated by comparing our results with available experimental data and other theoretical investigations. We confirm that the rare gas Xe atom is preferentially adsorbed on the top-site configuration on the Ni(111) surface too. Our approach based on the use of the Maximally Localized Wannier Functions also allow us to well characterize the bonds between graphene and Ni(111)., Comment: 3 figures

Motivated by the remarkable experimental control of synthetic gauge fields in ultracold atomic systems, we investigate the effect of an artificial Rashba spin-orbit coupling on the spin polarization of a two-dimensional repulsive Fermi gas. By using a variational many-body wavefunction, based on a suitable spinorial structure, we find that the polarization properties of the system are indeed controlled by the interplay between spin-orbit coupling and repulsive interaction. In particular, two main effects are found: 1) The Rashba coupling determines a gradual increase of the degree of polarization beyond the critical repulsive interaction strength, at variance with conventional 2D Stoner instability. 2) The critical interaction strength, above which finite polarization is developed, shows a dependence on the Rashba coupling, i.e. it is enhanced in case the Rashba coupling exceeds a critical value. A simple analytic expression for the critical interaction strength is further derived in the context of our variational formulation, which allows for a straightforward and insightful analysis of the present problem., Comment: 7 pages, 3 figures

This review of the research literature focuses on the interconnectedness of the roles of mentor teachers and pre-service teachers. In order to examine the interconnectedness of mentors and mentees, the paper firstly delves into what mentoring is and what contextual factors influence mentoring in pre-service teacher education. It then examines the research literature on mentors and mentees and the roles they undertake in a mentoring relationship. Emerging from the examination of the roles is identification of how the relationship functions with regard to the mentor and mentee who work together to achieve specific goals. The paper highlights the fact that limited research has examined mentor and mentees as interconnected partners in mentoring relationships. The paper outlines how the mentoring relationship participants can actively participate and interact. In conclusion, the paper provides a definition for mentoring that embraces essential mentoring components for pre-service teacher education contexts. (Contains 5 figures.)