The Role of Molecular Structure in Monte Carlo Simulations of the Secondary Electron Yield and Backscattering Coefficient from Methacrylic Acid.

In this paper, we show the influence of the chemical structure of four different conformers on the secondary electron emission and backscattering of an electron beam from a gel of methacrylic acid. The conformers have different permanent dipole moments, which determines the cross sections for elastic collisions with electrons. The cross sections are used in Monte Carlo simulations of an electron beam, which enters the gel of methacrylic acid. The secondary electron yield and the backscattering coefficient are computed as a function of the beam energy.

Mechanical Properties of Twisted Carbon Nanotube Bundles with Carbon Linkers from Molecular Dynamics Simulations.

The manufacturing of high-modulus, high-strength fibers is of paramount importance for real-world, high-end applications. In this respect, carbon nanotubes represent the ideal candidates for realizing such fibers. However, their remarkable mechanical performance is difficult to bring up to the macroscale, due to the low load transfer within the fiber. A strategy to increase such load transfer is the introduction of chemical linkers connecting the units, which can be obtained, for example, using carbon ion-beam irradiation. In this work, we investigate, via molecular dynamics simulations, the mechanical properties of twisted nanotube bundles in which the linkers are composed of interstitial single carbon atoms. We find a significant interplay between the twist and the percentage of linkers. Finally, we evaluate the suitability of two different force fields for the description of these systems: the dihedral-angle-corrected registry-dependent potential, which we couple for non-bonded interaction with either the AIREBO potential or the screened potential ReboScr2. We show that both of these potentials show some shortcomings in the investigation of the mechanical properties of bundles with carbon linkers.

Energy Deposition around Swift Carbon-Ion Tracks in Liquid Water.

Energetic carbon ions are promising projectiles used for cancer radiotherapy. A thorough knowledge of how the energy of these ions is deposited in biological media (mainly composed of liquid water) is required. This can be attained by means of detailed computer simulations, both macroscopically (relevant for appropriately delivering the dose) and at the nanoscale (important for determining the inflicted radiobiological damage). The energy lost per unit path length (i.e., the so-called stopping power) of carbon ions is here theoretically calculated within the dielectric formalism from the excitation spectrum of liquid water obtained from two complementary approaches (one relying on an optical-data model and the other exclusively on ab initio calculations). In addition, the energy carried at the nanometre scale by the generated secondary electrons around the ion's path is simulated by means of a detailed Monte Carlo code. For this purpose, we use the ion and electron cross sections calculated by means of state-of-the art approaches suited to take into account the condensed-phase nature of the liquid water target. As a result of these simulations, the radial dose around the ion's path is obtained, as well as the distributions of clustered events in nanometric volumes similar to the dimensions of DNA convolutions, contributing to the biological damage for carbon ions in a wide energy range, covering from the plateau to the maximum of the Bragg peak.

Understanding anharmonic effects on hydrogen desorption characteristics of MgnH2n nanoclusters by ab initio trained deep neural network.

Magnesium hydride (MgH2) has been widely studied for effective hydrogen storage. However, its bulk desorption temperature (553 K) is deemed too high for practical applications. Besides doping, a strategy to decrease such reaction energy for releasing hydrogen is the use of MgH2-based nanoparticles (NPs). Here, we investigate first the thermodynamic properties of MgnH2n NPs (n < 10) from first-principles, in particular by assessing the anharmonic effects on the enthalpy, entropy and thermal expansion by means of the stochastic self consistent harmonic approximation (SSCHA). This method goes beyond previous approaches, typically based on molecular mechanics and the quasi-harmonic approximation, allowing the ab initio calculation of the fully-anharmonic free energy. We find an almost linear dependence on temperature of the interatomic bond lengths - with a relative variation of few percent over 300 K - alongside with a bond distance decrease of the Mg-H bonds. In order to increase the size of MgnH2n NPs toward experiments of hydrogen desorption we devise a computationally effective machine learning model trained to accurately determine the forces and total energies (i.e. the potential energy surfaces), integrating the latter with the SSCHA model to fully include the anharmonic effects. We find a significative decrease of the H-desorption temperature for sub-nanometric clusters MgnH2n with n ≤ 10, with a non-negligible, although little effect due to anharmonicities (up to 10%).

Electronic excitation spectra of cerium oxides: from ab initio dielectric response functions to Monte Carlo electron transport simulations.

Nanomaterials made of cerium oxides CeO2 and Ce2O3 have a broad range of applications, from catalysts in automotive, industrial or energy operations to promising materials to enhance hadrontherapy effectiveness in oncological treatments. To elucidate the physico-chemical mechanisms involved in these processes, it is of paramount importance to know the electronic excitation spectra of these oxides, which are obtained here through high-accuracy linear-response time-dependent density functional theory calculations. In particular, the macroscopic dielectric response functions  of both bulk CeO2 and Ce2O3 are derived, which compare remarkably well with the available experimental data. These results stress the importance of appropriately accounting for local field effects to model the dielectric function of metal oxides. Furthermore, we reckon the energy loss functions Im(-1/) of the materials, including the accurate evaluation of the momentum transfer dispersion from first-principles calculations. In this respect, by using Mermin-type parametrization we are able to model the contribution of different electronic excitations to the dielectric loss function. Finally, from the knowledge of the electron inelastic mean free path, together with the elastic mean free path provided by the relativistic Mott theory, we carry out statistical Monte Carlo (MC) electron transport simulations to reproduce the major features of the reported experimental reflection electron energy loss (REEL) spectra of cerium oxides. The good agreement with REEL experimental data strongly supports our approach based on MC modelling, whose main inputs were obtained using ab initio calculated electronic excitation spectra in a broad range of momentum and energy transfers.

Relative Role of Physical Mechanisms on Complex Biodamage Induced by Carbon Irradiation.

The effective use of swift ion beams in cancer treatment (known as hadrontherapy) as well as appropriate protection in manned space missions rely on the accurate understanding of the energy delivery to cells that damages their genetic information. The key ingredient characterizing the response of a medium to the perturbation induced by charged particles is its electronic excitation spectrum. By using linear-response time-dependent density functional theory, we obtained the energy and momentum transfer excitation spectrum (the energy-loss function, ELF) of liquid water (the main constituent of biological tissues), which was in excellent agreement with experimental data. The inelastic scattering cross sections obtained from this ELF, together with the elastic scattering cross sections derived by considering the condensed phase nature of the medium, were used to perform accurate Monte Carlo simulations of the energy deposited by swift carbon ions in liquid water and carried away by the generated secondary electrons, producing inelastic events such as ionization, excitation, and dissociative electron attachment (DEA). The latter are strongly correlated with cellular death, which is scored in sensitive volumes with the size of two DNA convolutions. The sizes of the clusters of damaging events for a wide range of carbon-ion energies, from those relevant to hadrontherapy up to those for cosmic radiation, predict with unprecedented statistical accuracy the nature and relative magnitude of the main inelastic processes contributing to radiation biodamage, confirming that ionization accounts for the vast majority of complex damage. DEA, typically regarded as a very relevant biodamage mechanism, surprisingly plays a minor role in carbon-ion induced clusters of harmful events.

Secondary electron emission and yield spectra of metals from Monte Carlo simulations and experiments.

In this work, we present a computational method, based on the Monte Carlo statistical approach, for calculating electron energy emission and yield spectra of metals, such as copper, silver and gold. The calculation of these observables proceeds via the Mott theory with a Dirac-Hartree-Fock spherical potential to deal with the elastic scattering processes, and by using the Ritchie dielectric approach to model the electron inelastic scattering events. In the latter case, the dielectric function, which represents the starting point for the evaluation of the energy loss, is obtained from experimental reflection electron energy loss spectra. The generation of secondary electrons upon ionization of the samples is also implemented in the calculation. A remarkable agreement is obtained between both theoretical and experimental electron emission spectra and yield curves.

A novel combined experimental and multiscale theoretical approach to unravel the structure of SiC/SiOx core/shell nanowires for their optimal design.

In this work we propose a realistic model of nanometer-thick SiC/SiOx core/shell nanowires (NWs) using a combined first-principles and experimental approach. SiC/SiOx core/shell NWs were first synthesised by a low-cost carbothermal method and their chemical-physical experimental analysis was accomplished by recording X-ray absorption near-edge spectra. In particular, the K-edge absorption lineshapes of C, O, and Si are used to validate our computational model of the SiC/SiOx core/shell NW architectures, obtained by a multiscale approach, including molecular dynamics, tight-binding and density functional simulations. Moreover, we present ab initio calculations of the electronic structure of hydrogenated SiC and SiC/SiOx core/shell NWs, studying the modification induced by several different substitutional defects and impurities into both the surface and the interfacial region between the SiC core and the SiOx shell. We find that on the one hand the electron quantum confinement results in a broadening of the band gap, while hydroxyl surface terminations decrease it. This computational investigation shows that our model of SiC/SiOx core/shell NWs is capable to deliver an accurate interpretation of the recorded X-ray absorption near-edge spectra and proves to be a valuable tool towards the optimal design and application of these nanosystems in actual devices.

Ultrafast Carotenoid to Retinal Energy Transfer in Xanthorhodopsin Revealed by the Combination of Transient Absorption and Two-Dimensional Electronic Spectroscopy.

By comparing two-dimensional electronic spectroscopy (2DES) and Pump-Probe (PP) measurements on xanthorhodopsin (XR) and reduced-xanthorhodopsin (RXR) complexes, the ultrafast carotenoid-to-retinal energy transfer pathway is revealed, at very early times, by an excess of signal amplitude at the associated cross-peak and by the carotenoid bleaching reduction due to its ground state recovery. The combination of the measured 2DES and PP spectroscopic data with theoretical modelling allows a clear identification of the main experimental signals and a comprehensive interpretation of their origin and dynamics. The remarkable velocity of the energy transfer, despite the non-negligible energy separation between the two chromophores, and the analysis of the underlying transport mechanism, highlight the role played by the ground state carotenoid vibrations in assisting the process.

UV-Light-Induced Vibrational Coherences: The Key to Understand Kasha Rule Violation in trans-Azobenzene.

We combine sub-20 fs transient absorption spectroscopy with state-of-the-art computations to study the ultrafast photoinduced dynamics of trans-azobenzene (AB). We are able to resolve the lifetime of the ππ* state, whose decay within ca. 50 fs is correlated to the buildup of the nπ* population and to the emergence of coherences in the dynamics, to date unobserved. Nonlinear spectroscopy simulations call for the CNN in-plane bendings as the active modes in the subps photoinduced coherent dynamics out of the ππ* state. Radiative to kinetic energy transfer into these modes drives the system to a high-energy planar nπ*/ground state conical intersection, inaccessible upon direct excitation of the nπ* state, that triggers an ultrafast (0.45 ps) nonproductive decay of the nπ* state and is thus responsible for the observed Kasha rule violation in UV excited trans-AB. On the other hand, cis-AB is built only after intramolecular vibrational energy redistribution and population of the NN torsional mode.

2D Material Armors Showing Superior Impact Strength of Few Layers.

We study the ballistic properties of two-dimensional (2D) materials upon the hypervelocity impacts of C60 fullerene molecules combining ab initio density functional tight binding and finite element simulations. The critical penetration energy of monolayer membranes is determined using graphene and the 2D allotrope of boron nitride as case studies. Furthermore, the energy absorption scaling laws with a variable number of layers and interlayer spacing are investigated, for homogeneous or hybrid configurations (alternated stacking of graphene and boron nitride). At the nanolevel, a synergistic interaction between the layers emerges, not observed at the micro- and macro-scale for graphene armors. This size-scale transition in the impact behavior toward higher dimensional scales is rationalized in terms of scaling of the damaged volume and material strength. An optimal number of layers, between 5 and 10, emerges demonstrating that few-layered 2D material armors possess impact strength even higher than their monolayer counterparts. These results provide fundamental understanding for the design of ultralightweight multilayer armors using enhanced 2D material-based nanocomposites.

A Quantum Chemical Interpretation of Two-Dimensional Electronic Spectroscopy of Light-Harvesting Complexes.

Nonlinear electronic spectroscopies represent one of the most powerful techniques to study complex multichromophoric architectures. For these systems, in fact, linear spectra are too congested to be used to disentangle the many coupled vibroelectronic processes that are activated. By using a 2D approach, instead, a clear picture can be achieved, but only when the recorded spectra are combined with a proper interpretative model. So far, this has been almost always achieved through parametrized exciton Hamiltonians that necessarily introduce biases and/or arbitrary assumptions. In this study, a first-principles approach is presented that combines accurate quantum chemical descriptions with state-of-the-art models for the environment through the use of atomistic and polarizable embeddings. Slow and fast bath dynamics, along with exciton transport between the pigments, are included. This approach is applied to the 2DES spectroscopy of the Light-Harvesting 2 (LH2) complex of purple bacteria. Simulations are extended over the entire visible-near-infrared spectral region to cover both carotenoid and bacteriochlorophyll signals. Our results provide an accurate description of excitonic properties and relaxation pathways, and give an unprecedented insight into the interpretation of the spectral signatures of the measured 2D signals.

Lobachevsky crystallography made real through carbon pseudospheres.

We realize Lobachevsky geometry in a simulation lab, by producing a carbon-based energetically stable molecular structure, arranged in the shape of a Beltrami pseudosphere. We find that this structure: (i) corresponds to a non-Euclidean crystallographic group, namely a loxodromic subgroup of SL(2, Z); (ii) has an unavoidable singular boundary, that we fully take into account. Our approach, substantiated by extensive numerical simulations of Beltrami pseudospheres of different size, might be applied to other surfaces of constant negative Gaussian curvature, and points to a general procedure to generate them. Our results also pave the way to test certain scenarios of the physics of curved spacetimes owing to graphene's unique properties.

Tetrapeptide unfolding dynamics followed by core-level spectroscopy: a first-principles approach.

In this work we demonstrate that core level analysis is a powerful tool for disentangling the dynamics of a model polypeptide undergoing conformational changes in solution and disulphide bond formation. In particular, we present computer simulations within both initial and final state approximations of 1s sulphur core level shifts (S1s CLS) of the CYFC (cysteine-phenylalanine-tyrosine-cysteine) tetrapeptide for different folding configurations. Using increasing levels of accuracy, from Hartree-Fock and density functional theory to configuration interaction via a multiscale algorithm capable of reducing drastically the computational cost of electronic structure calculations, we find that distinct peptide arrangements present S1s CLS sizeably different (in excess of 0.5 eV) with respect to the reference disulfide bridge state. This approach, leading to experimentally detectable signals, may represent an alternative to other established spectroscopic techniques.

Computational study of graphene growth on copper by first-principles and kinetic Monte Carlo calculations.

In this work the growth of a graphene monolayer on copper substrate, as typically achieved via chemical vapor deposition of propene (C3H6), was investigated by first-principles and kinetic Monte Carlo calculations. A comparison between calculated C1s core-level binding energies and electron spectroscopy measurements showed that graphene nucleates from isolated carbon atoms adsorbed on surface defects or sub-superficial layers upon hydrocarbon fragmentation. In this respect, ab initio nudged elastic band simulations yield the energetic barriers characterizing the diffusion of elemental carbon on the Cu(111) surface and atomic carbon uptake by the growing graphene film. Our calculations highlight a strong interaction between the growing film edges and the copper substrate, indicative of the importance of the grain boundaries in the epitaxy process. Furthermore, we used activation energies to compute the reaction rates for the different mechanisms occurring at the carbon-copper interface via harmonic transition state theory. Finally, we simulated the long-time system growth evolution through a kinetic Monte Carlo approach for different temperatures and coverage. Our ab initio and Monte Carlo simulations of the out-of-equilibrium system point towards a growth model strikingly different from that of standard film growth. Graphene growth on copper turns out to be a catalytic, thermally-activated process that nucleates from carbon monomers, proceeds by adsorption of carbon atoms, and is not self-limiting. Furthermore, graphene growth seems to be more effective at carbon supersaturation of the surface-a clear fingerprint of a large activation barrier for C attachment. Our growth model and computational results are in good agreement with recent X-ray photoelectron spectroscopy experimental measurements.

Non-adiabatic ab initio molecular dynamics of supersonic beam epitaxy of silicon carbide at room temperature.

In this work, we investigate the processes leading to the room-temperature growth of silicon carbide thin films by supersonic molecular beam epitaxy technique. We present experimental data showing that the collision of fullerene on a silicon surface induces strong chemical-physical perturbations and, for sufficient velocity, disruption of molecular bonds, and cage breaking with formation of nanostructures with different stoichiometric character. We show that in these out-of-equilibrium conditions, it is necessary to go beyond the standard implementations of density functional theory, as ab initio methods based on the Born-Oppenheimer approximation fail to capture the excited-state dynamics. In particular, we analyse the Si-C(60) collision within the non-adiabatic nuclear dynamics framework, where stochastic hops occur between adiabatic surfaces calculated with time-dependent density functional theory. This theoretical description of the C(60) impact on the Si surface is in good agreement with our experimental findings.

Epitaxy of nanocrystalline silicon carbide on Si(111) at room temperature.

Silicon carbide (SiC) has unique chemical, physical, and mechanical properties. A factor strongly limiting SiC-based technologies is the high-temperature synthesis. In this work, we provide unprecedented experimental and theoretical evidence of 3C-SiC epitaxy on silicon at room temperature by using a buckminsterfullerene (C(60)) supersonic beam. Chemical processes, such as C(60) rupture, are activated at a precursor kinetic energy of 30-35 eV, far from thermodynamic equilibrium. This result paves the way for SiC synthesis on polymers or plastics that cannot withstand high temperatures.