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We developed a physics-informed deep neural network architecture able to achieve signal-to-noise ratio improvements starting from low-exposure noisy data. Our model is based on the nature of the photon detection process characterized by a Poisson probability distribution, an information which we included in the training loss function. Our approach surpasses previous algorithm performance for microscopy images; moreover, the generality of the physical concepts employed here, makes it readily exportable to any imaging context.

We developed a physics-informed deep neural network architecture able to achieve signal to noise ratio improvements starting from low exposure noisy data. Our model is based on the nature of the photon detection process characterized by a Poisson probability distribution which we included in the training loss function. Our approach surpasses previous algorithms performance for microscopy data, moreover, the generality of the physical concepts employed here, makes it readily exportable to any imaging context

Recent evidences show the growing importance of mechanical forces in directing basic processes in cellular functions through the complex scenario of mechanotransduction. In this context, however, the impact of chromatin physical state on cellular structure and function requires further study. Here, we characterized the effects of a loss-of-function mutation of MLL4, a chromatin regulator, on nuclear mechanical and structural properties. Measurements of such features in intact cells are to date challenging, as current gold-standard methods for mechanobiology cannot have access to subcellular structures: a complete characterization of their nuclear mechanical fingerprint is hence still elusive. By exploiting the innovative all-optical technique of Brillouin microscopy in our custom-made optical setup, we measured with three-dimensional sub-micrometric resolution the effects of MLL4-dependent mechanical stress on the nucleus of mesenchymal stem cells in different conditions. These results show the importance of mechanotransduction for vital cellular processes and pave the way towards the use of Brillouin microscopy as a reliable tool for medical diagnostic purposes of chromatinopathies, this mutation being involved in Kabuki syndrome, a severe genetic disease.

We developed a physics-informed deep neural network architecture able to achieve signal to noise ratio improvements starting from low exposure noisy data. Our model is based on the nature of the photon detection process characterized by a Poisson probability distribution which we included in the training loss function. Our approach surpasses previous algorithms performance for microscopy data, moreover, the generality of the physical concepts employed here, makes it readily exportable to any imaging context.

Dissociative and molecular water adsorption on the anatase (001) surface is studied in the context of state-of-the-art density functional theory in large supercells suited for adsorption studies at various water coverage ratios. At low coverage values below 1/4 ML, water adsorption remains dissociative and a network of hydrogen bonds between the so formed hydroxyl groups favors the formation of a ridge surface structure. The hydroxyl patterned (4 × 4) surface thus undergoes a (2 × 4) reconstruction that causes the relief of the large tensile stress measured in the unreconstructed surface along the direction orthogonal to the ridge. This phenomenology is accompanied by the loss of reactivity of the reconstructed surface with respect to the dissociative water adsorption that becomes molecular above 1/4 ML. We also show that the molecular adsorption on the terrace is weaker than the one on the ridge. The present water reconstruction model is discussed and compared to the well-known ADM model of the reconstru...

Supramolecular architectures involving DNA bases can have a strong impact in several fields such as nanomedicine and nanodevice manufacturing. To date, in addition to the four canonical nucleobases (adenine, thymine, guanine and cytosine), four other forms of cytosine modified at the 5 position have been identified in DNA. Among these four new cytosine derivatives, 5-carboxylcytosine has been recently discovered in mammalian stem cell DNA, and proposed as the final product of the oxidative epigenetic demethylation pathway on the 5 position of cytosine. In this work, a calcium salt of 5-carboxylcytosine has been synthesized and deposited on graphite surface, where it forms self-assembled features as long range monolayers and up to one micron long filaments. These structures have been analyzed in details combining different theoretical and experimental approaches: X-ray single-crystal diffraction data were used to simulate the molecule-graphite interaction, first using molecular dynamics and then refining the results using density functional theory (DFT); finally, data obtained with DFT were used to rationalize atomic force microscopy (AFM) results.

Damage formation is investigated in GaAs implanted with 1 MeV Si ions to ion fluences from $3\ifmmode\times\else\texttimes\fi{}{10}^{12}$ to $5\ifmmode\times\else\texttimes\fi{}{10}^{15}\phantom{\rule{4pt}{0ex}}{\mathrm{cm}}^{\ensuremath{-}2}$ at room temperature. Under the conditions applied, amorphization of the implanted layers does not occur. The weakly damaged layers are studied by applying different experimental techniques including Rutherford backscattering spectrometry in channeling configuration, x-ray diffraction, in situ curvature measurement, optical subgap spectroscopy, and transmission electron microscopy. The results are evaluated and quantitatively connected with each other. Damage formation is described as a function of the ion fluence using a common defect evolution model. Point defects and defect clusters have to be taken into account in the ion fluence range of main interest up to $2\ifmmode\times\else\texttimes\fi{}{10}^{15}\phantom{\rule{4pt}{0ex}}{\mathrm{cm}}^{\ensuremath{-}2}$. Point defects contribute by a factor of about 8 more to both perpendicular strain and in-plane stress than defect clusters. When the concentration of point defects or the induced strain reaches a critical value, defect clusters form, which ensures that no further increase of perpendicular strain occurs. This reveals a clear driving force for cluster formation. The microstructure of the defect clusters cannot be determined from the results. ${\mathrm{As}}_{3}{\mathrm{Ga}}_{2}$ interstitial clusters are supposed. A remarkable decrease of the shear modulus of the implanted layers below the value of pristine GaAs by $\ensuremath{\approx}\ensuremath{-}35%$ is observed. Surprisingly, the change of shear modulus already sets in at a very low damage level of a few percent.

Using first principles calculations based on density functional theory, the electronic, vibrational and superconducting properties of compounds with different stoichiometry ratios in the A15 phase have been studied. To this purpose, the λ mass enhancement parameter, which determines the superconducting critical temperature through the Allen-Dynes modification of the McMillan formula, has been explicitly calculated in the context of the density functional perturbation theory that allows the calculation of the matrix elements of the electron-phonon interactions at different compositions related to the Sn content. Our results provide a better understanding of the inhomogeneous composition of one of the most widely employed low-temperature superconductors, evidencing the electronic properties and the phonon modes that are responsible for the critical temperature degradation as the Sn concentration is varied. © the Owner Societies 2016.

Solid-state nanopores and nanogaps are emerging as promising tools for single molecule analysis. 2D materials, such as graphene, can potentially reach the spatial resolution needed for nucleic acid and protein sequencing. In the context of the density functional theory, atomistic modeling and non-equilibrium Green's function calculation, we show that glycine based polypeptide chains translocating across a nano-gap between two semi-infinite graphene nano-ribbons leave a specific transverse current signature for each peptide bond. The projected density of states and bond current analyses reveal a complex scenario with a role played by the adjacent α-carbons and side chains and by the orbitals of the partially resonant double bond involving C, N and O atoms of the peptide bond. In this context, specific fingerprints of the atoms involved in the peptide bonds are found. The same scenario is evidenced also for peptides involving alanine residues. The signal measured can be considered as a specific fingerprint of peptide bonds between small and neutral amino acids with no polar/charge effects. On this basis, a newly conceived nano-device made of a graphene based array of nano-gap is proposed as a possible route to approach peptide sequencing with atomic resolution.

Novel nanomaterial systems as possible candidates for gate dielectric insulators play a key role in the fabrication of next-generation transistor devices in both metal-oxide-semiconductor (MOSFET) and organic thin-film transistors (OTFTs). We focus on one of these new alternative gate dielectric nanostructured materials: self-assembled monolayers (SAMs) of hydroxylated octadecyltrichlorosilane (OTS) chains deposited on a (111) Si substrate. Starting from the evaluation of the surface partial dipole of the SAM coating on the Si surface, we report a quantitative ab initio study of the static dielectric constant of the OTS thin-film coating at different coverage values of the hydrogenated (111) Si surface ranging from partial to full coverage. The main physical features of the OTS SAM films at different coverages have been studied with respect to their influence on the static dielectric constant, and a two-layer model is established. A linear dependence of the static dielectric constant versus the coverage i...

We report on the investigations of the structural and superconducting properties of Nb3Sn in the GPa range by angular dispersive synchrotron X-ray diffraction and ab-initio calculations based on density functional theory. X-ray Diffraction experiments were carried out on Nb3Sn technological samples to explore the equation of state at room temperature and at pressures up to 43.5 GPa: We observe an anomaly in the P-V curve in the region 5-10 GPa. The ab-initio calculated lattice parameter of Nb3 Sn as a function of pressure has been used as an input for the calculation of the phonon dispersion curves and of the electronic band structures along different high-symmetry directions in the Brillouin zone. The critical temperature has been calculated as a function of the hydrostatic pressure by means of the Allen-Dynes modification of the McMillan formula: We found that its behavior is dictated mostly by the electronic contribution, but evident anomalies up to 6 GPa arise from phonons. These findings are a clue that Nb3 Sn could have some structural instabilities with impact on its superconducting properties when subjected to a pressure of a few GPa and they represent an important step to understand and optimize the performances of Nb3Sn materials under the hard operational conditions of high field superconducting magnets. © 2002-2011 IEEE.

First principles calculations based on density functional theory, density functional perturbation theory and many body perturbation theory are employed to explain the optical absorption peak of a newly synthesized oligo-tiophene molecule that has been considered for bulk-heterojunction solar cells. The GW approach is used to obtain quasiparticle energies as a pre-requisite to solve the Bethe-Salpeter equation for the excitonic Hamiltonian, while density functional perturbation theory, in conjunction with the Huang-Rhys method, have been employed to calculate the vibration assisted ionization spectrum.

The adsorption properties of TiO2 surfaces with biological environments have shown to be very important for bio-compatibility properties. Interactions of biological molecules with inorganic materials in aqueous systems, are mediated by water molecules. Hence the understanding of the possible conformations that water molecules can assume on the inorganic surfaces it is very important. Many studies concerning the structural conformations of adsorbed water molecules on rutile and anatase, the most likely exposed surface phases, show that the first layer of adsorbed water molecules play a crucial role in mediating the structural and physical properties of the upper interacting environment layers. In this contest we performed a detailed analysis of the possible conformations of the first layer of water molecules adsorbed on the (101) TiO2 surface; total energy calculations and NEB techniques, in contest of the DFT theory, has been used to study the stability and the diffusion properties as a further insight of...

First principles calculations based on density functional theory and many body perturbation theory have been employed to study the optical absorption properties of a newly synthesized oligo-thiophene molecule, with a quaterthiophene central unit, that has been designed for solution-processed bulk-heterojunction solar cells. To this aim we have employed the GW approach to obtain quasiparticle energies as a pre-requisite to solve the Bethe-Salpeter equation for the excitonic Hamiltonian. We show that the experimental absorption spectrum can be explained only by taking into account the inter-molecular transitions among the π-stacked poly-conjugated molecules that are typically obtained in solid-state organic samples.

N-Heterocyclic carbenes (NHCs) are widely used as organocatalysts. Their reactivity (and instability) is related to their basicity and nucleophilicity, which, in turn, are linked to their scaffold. NHCs can be generated by chemical deprotonation or electrochemical reduction of the parent azolium cations, NHCH+s. Cyclic voltammetry enabled the reduction potential of the NHCH+s to be determined; the reduction potential is related to the acidity of the NHCH+s and the oxidation potential of the NHCs, which is related to the nucleophilicity of the NHCs. It was thus possible to order different NHCH+s and NHCs by their acidity and nucleophilicity, respectively. A study on the stability of NHCs was also performed in the absence and in the presence of acetic acid to assess the possibility of the coexistence of NHC and an acid in the same solution, opening the possibility of co-catalysis. Finally, ab initio calculations confirmed the presence, in DMF, of hydrogen-bonded NHCH+ –NHC adducts, which could influence catalyst activity.

(101) anatase TiO2 surface in water ambient is an important system for the interaction of biocompatible nanodevices with biological environment. Following the experimental evidence showing that water molecules are mobile at temperature as low as 190 K and tend to form clusters along the [111]/[111] surface directions, a complete theoretical characterization of the dynamical properties of the first water layer on the (101) anatase TiO2 surface is presented. A variety of computational techniques have been employed in the context of the transition-state theory in the harmonic regime, ranging from first-principles total energy ground-state calculations, to density functional perturbation theory, minimum energy path search, and kinetic Monte Carlo simulations, to explain the experimental results on water kinetics on the (101) anatase TiO2 surface. We have calculated the migration energy barrier of water molecules, the vibrational prefactor through the phonon density of states, and the hopping rate along two pr...

The catalytic properties of thermally distorted single wall carbon nanotubes for the methane dissociation reaction have been investigated in the framework of semi-empirical tight-binding molecular dynamics, electronic structure and total energy calculations. It is shown that, if methane molecules and the nanotube are allowed to get closer than the equilibrium physi-sorption distance, the next dissociation reaction step is characterized by a small enthalpy change. Moreover the reactivity hierarchy of the various carbon nanotubes considered is related to the electronic density of states originating from the axial components of the atomic orbitals.

The interface of biological molecules with inorganic surfaces has been the subject of several recent studies. Experimentally some amino acids are evidenced to play a critical role in the adhesion and selectivity on oxide surfaces; however, detailed information on how the water molecules on the hydrated surface are able to mediate the adsorption is still missing. Accurate total energy ab initio calculations based on dispersion-corrected density functional theory have been performed to investigate the adsorption of selected amino acids on the hydrated ZnO(101¯0) surface, and the results are presented and discussed in this paper. We have also investigated the role played by water in the determination of the most energetically favorable adsorption configurations of the selected amino acids. We have found that for some amino acids the most energetically favorable configurations involve the deprotonation of the molecule if the water screening is not effective. © 2015 American Chemical Society.

Arg, Lys and Asp amino acids are known to play a critical role in the adhesion of the RKLPDA engineered peptide on the (101) surface of the titania anatase phase. To understand their contribution to peptide adhesion, we have considered the relevant charge states due to protonation (Arg and Lys) or deprotonation (Asp) occurring in neutral water solution, and studied their adsorption on the (101) anatase TiO2 surface by ab initio total energy calculations based on density functional theory. The adsorption configurations on the hydrated surface are compared to those on the dry surface considering also the presence of the hydration shell around amino acid side-chains. This study explains how water molecules mediate the adsorption of charged amino acids showing that protonated amino acids are chemically adsorbed much more strongly than de-protonated Asp. Moreover it is shown that the polar screening of the hydration shell reduces the adsorption energy of the protonated amino acids to a small extent, thus evidencing that both Arg and Lys strongly adhere on the (101) anatase TiO2 surface in neutral water solution and that they play a major role in the adhesion of the RKLPDA peptide.

Compatibility between biological molecules and inorganic materials, such as crystalline metal oxides, is strongly dependent on the selectivity properties and the adhesion processes at the interface between the two systems. Among the many different aspects that affect the adsorption processes of peptides or proteins onto inorganic surfaces, such as the charge state of the amino acids, the peptide 3D structure, the surface roughness, the presence of vacancies or defects on and below the surface, a key role is certainly played by the water solvent whose molecules mediate the interaction. Then the surface hydration pattern may strongly affect the adsorption behavior of biological molecules. For the particular case of (101) anatase TiO2 surface that has a fundamental importance in the interaction of biocompatible nano-devices with biological environment, it was shown, both theoretically and experimentally, that various hydration patterns are close in energy and that the water molecules are mobile at as low tem...

Arg, Lys and Asp amino acids are known to play a critical role in the adhesion of the RKLPDA engineered peptide on the (101) surface of the titania anatase phase. To understand their contribution to peptide adhesion, we have considered the relevant charge states due to protonation (Arg and Lys) or deprotonation (Asp) occurring in neutral water solution, and studied their adsorption on the (101) anatase TiO2 surface by ab initio total energy calculations based on density functional theory. The adsorption configurations on the hydrated surface are compared to those on the dry surface considering also the presence of the hydration shell around amino acid side-chains. This study explains how water molecules mediate the adsorption of charged amino acids showing that protonated amino acids are chemically adsorbed much more strongly than de-protonated Asp. Moreover it is shown that the polar screening of the hydration shell reduces the adsorption energy of the protonated amino acids to a small extent, thus evidencing that both Arg and Lys strongly adhere on the (101) anatase TiO2 surface in neutral water solution and that they play a major role in the adhesion of the RKLPDA peptide.

Many nano-material systems are currently under consideration as possible candidates for gate dielectric insulators in both metal-oxide-semiconductor (MOSFET) and organic (OFET) field-effect transistors. In this contribution, the possibility of employing self-assembled monolayers (SAMs) of hydroxylated octadecyltrichlorosilane (OTS) chains on a (111) Si substrate as gate dielectrics is discussed; in particular ab initio theoretical simulations have been employed to study the structural properties, work function modifications, and the insulating properties of OTS thin film coatings on Si substrates.

The adhesion configurations and coverage of self-assembled monolayers (SAMs) of hydroxylated octadecyltrichlorosilane (OTS) chains on a (111) Si substrate have been studied by ab initio total energy calculations, focusing on the work function calculation for coatings with partial and full coverage. Multiple covalent attachments per molecule with the Si substrate have also been considered as possible sources of irregularities and disorder of the coating, demonstrating a relevant change in the work function. A linear dependence of the work function with respect to the surface partial dipole has been established, allowing the extrapolation of the work function to full coverage using a simple toy model. For all the adsorption configurations examined, moreover, we find that the electron work function of the coated surface is lowered with respect to the hydrogenated Si, thus increasing the hole isolation behavior.

Carbon nanostructures are currently under investigation as possible ideal media for gas storage and mesoporous materials for gas sensors. The recent scientific literature concerning gas adsorption in nanocarbons, however, is affected by a significant variation in the experimental data, mainly due to the different characteristics of the investigated samples arising from the variety of the synthesis techniques used and their reproducibility. Atomistic simulations have turned out to be sometimes crucial to study the properties of these systems in order to support the experiments, to indicate the physical limits inherent in the investigated structures, and to suggest possible new routes for application purposes. In consideration of the extent of the theme, we have chosen to treat in this paper the results obtained within some of the most popular atomistic theoretical frameworks without any purpose of completeness. A significant part of this paper is dedicated to the hydrogen adsorption on C-based nanostructures for its obvious importance and the exceptional efforts devoted to it by the scientific community.

Hydrophobic coatings, such as octadecyltrichlorosilane or n-alkyl monolayers, enhance the slippage of liquids on solid walls. For a given alkyl chain length, the main structural parameter for homogeneous coatings is the tilt angle between coating molecules and the surface normal. In this paper, ab initio calculations are used to calculate the equilibrium configuration of coating molecules, showing that the tilt angle easily changes from 0 ° to 30 ° depending on the specific head group binding the solid substrate. These values are used to set up classical molecular dynamics of water slippage over the coatings using different water models (Transferable Intermolecular Potential 3 point (TIP3P), Transferable Intermolecular Potential 4 point (TIP4P) and TIP4P/2005). The slippage is found to be robust with respect to the coating tilting, while a slight dependence on the water model is observed.

The first stage functionalization of hydrogenated (111) Si surface with methyl-terminated monolayers to form hydrophobic coatings has been studied by accurate ab initio density functional total energy calculations. The first stage adsorption events involving one or two deposited $n$-alkane and $n$-alkyl-silane molecules have been characterized from the geometrical and the energetic points of view; the ground-state adsorption configurations together with the geometrical and the energetic parameters relevant to self-assembling processes have been obtained, such as the polymers tilt angles, the rotation energy barriers, the binding energies, and the electrostatic interactions. The above-mentioned quantities have been related to the stability properties of self-assembled monolayers and have been recognized to affect critically the stability and the uniformity of the hydrophobic film elucidating the reasons why some commonly used polymers behave differently.

Stable intrinsic di-interstitials configurations in GaAs with different stoichiometric compositions are studied by first principles total-energy calculations. For each composition, fully relaxed stable and metastable structures have been obtained at different charge states to study the stability properties in different doping conditions and calculate the thermodynamic transition states, showing that the studied structures are stable against the isolated interstitials with large binding energies. The structural and electronic properties of the different configurations are also discussed in order to determine the relevant observables and to plan for possible future experiments aimed to detect them. In this context, we have focused particularly on different Ga di-interstitials configurations showing that the most stable one can be detected by means of state of the art deep level detection techniques, whereas more sophisticated experiments are required, involving symmetry and thermal activation processes, to detect As di-interstitials. Combining the different techniques in an sort of “differential diagnosis,” at least two of the three possible, stoichiometry dependent, di-interstitial configurations can be identified.

Intrinsic interstitials in $\mathrm{GaAs}$ are known to have a large formation energy that makes their concentration almost negligible in as-grown materials. However, interstitials must be explicitly considered in implanted $\mathrm{GaAs}$ where collision cascades, induced by the energetic ions, produce a large amount of Frenkel defects: these, indeed, can be considered as a source of interstitials that can migrate and evolve in larger aggregates. Due to the wide relaxation pattern induced by intrinsic interstitials, large supercells are necessary to avoid artifacts that, in practice, make first-principles calculations too computationally demanding, even for complexes involving just three interstitials. Following previous papers on di-interstitials, this paper reports on the structural, stability, and electronic properties of ${I}_{3}$ complexes, depending on the topology and the stoichiometry, approached by semiempirical tight-binding molecular dynamics and damped dynamics. ${I}_{3}$ complexes reveal a strong tendency to form these structures, and a stability hierarchy is determined between them. All the stable and metastable structures have been studied regarding the electronic structure, the charge distribution through the Mulliken analysis, the localization of the defect related wave function, and the local lattice strain field around the complex. The present study is aimed to define the selection rules that must be considered in order to build up larger ${I}_{n}$ (with $n\ensuremath{\ge}4$) self-interstitials complexes in $\mathrm{GaAs}$.

Methane adsorption at Ca decorated single wall carbon nanotubes has been studied by ab initio total energy calculations based on the density functional theory. The adsorption configurations have been studied by using various exchange-correlation energy functionals also including two possible long-range interaction correction schemes. Our calculations show that methane adsorption at Ca decorated carbon nanotubes is markedly enhanced when impurity atoms are considered as individual adsorption sites. We demonstrate that up to six CH4 molecules can bind at a single Ca impurity at room temperature. The phenomenon responsible for the measured adsorption energy is recognized as a Kubas-type interaction that involves the orbital overlap between the Ca d state and the methane σ molecular orbitals. The adsorption values obtained with the different energy functionals used are discussed showing that local density approximation, often employed in the recent literature for similar adsorption problems, is affected by severe limitations when orbital overlap and physisorption co-exist. Lastly the well-known problem of Ca clustering is studied and discussed showing that, different from the hydrogen case, it does not induce any molecular dissociation.

The recent discovery of intrinsic di-interstitial stability against the isolated self-interstitial point defects in GaAs has evidenced the importance of such complexes in, for instance, irradiated GaAs. In this paper, we illustrate and discuss diffusion of such complexes in comparison with isolated self-interstitials. In particular, the diffusion barriers of neutral di-interstitials have been calculated in the framework of density functional theory, showing that, in addition to their being stable, di-interstitials can also diffuse rapidly through the lattice, similarly to isolated self-interstitials.