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Carbon nanodots (CNDs) are the latest and most shining rising stars among photoluminescent (PL) nanomaterials. These carbon-based surface-passivated nanostructures compete with other related PL materials, including traditional semiconductor quantum dots and organic dyes, with a long list of benefits and emerging applications. Advantages of CNDs include tunable inherent optical properties and high photostability, rich possibilities for surface functionalization and doping, dispersibility, low toxicity, and viable synthesis (top-down and bottom-up) from organic materials. CNDs can be applied to biomedicine including imaging and sensing, drug-delivery, photodynamic therapy, photocatalysis but also to energy harvesting in solar cells and as LEDs. More applications are reported continuously, making this already a research field of its own. Understanding of the properties of CNDs requires one to go to the levels of electrons, atoms, molecules, and nanostructures at different scales using modern molecular modeling and to correlate it tightly with experiments. This review highlights different in silico techniques and studies, from quantum chemistry to the mesoscale, with particular reference to carbon nanodots, carbonaceous nanoparticles whose structural and photophysical properties are not fully elucidated. The role of experimental investigation is also presented. Hereby, we hope to encourage the reader to investigate CNDs and to apply virtual chemistry to obtain further insights needed to customize these amazing systems for novel prospective applications.

The increasing energy demand and the ever more pressing need for clean technologies of energy conversion pose one of the most urgent and complicated issues of our age. Thermoelectricity, namely the direct conversion of waste heat into electricity, is a promising technique based on a long-standing physical phenomenon, which still has not fully developed its potential, mainly due to the low efficiency of the process. In order to improve the thermoelectric performance, a huge effort is being made by physicists, materials scientists and engineers, with the primary aims of better understanding the fundamental issues ruling the improvement of the thermoelectric figure of merit, and finally building the most efficient thermoelectric devices. In this Roadmap an overview is given about the most recent experimental and computational results obtained within the Italian research community on the optimization of composition and morphology of some thermoelectric materials, as well as on the design of thermoelectric and hybrid thermoelectric/photovoltaic devices.

Non-equilibrium molecular dynamics simulations have been applied to study thermal transport properties, such as thermal conductivity and rectification, in nanoporous Si membranes. Cylindrical pores have been generated in crystalline Si membranes with different configurations, including step-like, ordered and random pore distributions. The effect of interface and overall porosity on thermal transport properties has been investigated as well as the impact of the porosity profile on the direction of the heat current. The lowest thermal conductivity and highest thermal rectification for equal porosity have been found for a step-like pore distribution. Increasing interface porosity resulted in an increase of thermal rectification, which has been found to be systematically higher for random pore distribution with respect to an ordered one. Furthermore, a maximum in rectification of 5.5% has been found for a specific overall porosity (

The molecular emission model is the most accredited one to explain the emission properties of carbon dots (CDs) in a low-temperature bottom-up synthesis approach. In the case of citric acid and ure...

We study by scanning thermal microscopy the nanoscale thermal conductance of films (40-400 nm thick) of [1]benzothieno[3,2-b][1]benzothiophene (BTBT) and 2,7-dioctyl[1]benzothieno[3,2-b][1]benzothiophene (C8-BTBT-C8). We demonstrate that the out-of-plane thermal conductivity is significant along the interlayer direction, larger for BTBT (0.63 ± 0.12 W m-1 K-1) compared to C8-BTBT-C8 (0.25 ± 0.13 W m-1 K-1). These results are supported by molecular dynamics calculations (approach to equilibrium molecular dynamics method) performed on the corresponding molecular crystals. The calculations point to significant thermal conductivity (3D-like) values along the 3 crystalline directions, with anisotropy factors between the crystalline directions below 1.8 for BTBT and below 2.8 for C8-BTBT-C8, in deep contrast with the charge transport properties featuring a two-dimensional character for these materials. In agreement with the experiments, the calculations yield larger values in BTBT compared to C8-BTBT-C8 (0.6-1.3 W m-1 K-1versus 0.3-0.7 W m-1 K-1, respectively). The weak thickness dependence of the nanoscale thermal resistance is in agreement with a simple analytical model. This journal is, M. G., D. G., S. L. and D. V. thank the ANR for financial support (ANR-16-CE05-0029). Y. G. is thankful to the Belgian National Fund for Scientific Research (FNRS) for financial support through research projects BTBT (# 2.4565.11), Phasetrans (# T.0058.14), Pi-Fast (# T.0072.18), 2D to 3D (# 30489208), and DIFFRA (# U.G001.19). Financial supports from the French Community of Belgian (ARC # 20061) is also acknowledged. G. S. acknowledges postdoctoral fellowship support from the FNRS. The work in the Laboratory for Chemistry of Novel Materials was supported by the Consortium des Équipements de Calcul Intensif (CÉCI), funded by the Fonds de la Recherche Scientifique de Belgique (F.R.S.-FNRS) under grant # 2.5020.11. J.C. and A.V. are FNRS research fellows.

Second sound is known as the thermal transport regime occurring in a wave-like fashion, usually identified in a limited number of materials only at cryogenic temperatures. Here we show that second sound in a μm-long carbon chain (cumulene) might occur even at room temperature. To this aim, we calibrate a many-body force field on the first principles calculated phonon dispersion relations of cumulene and, through molecular dynamics, we mimic laser-induced transient thermal grating experiments. We provide evidence that by tuning temperature as well as the space modulation of its initial profile we can reversibly drive the system from a wave-like to a diffusive-like thermal transport. By following three different theoretical methodologies (molecular dynamics, the Maxwell-Cattaneo-Vernotte equation, and heat transport microscopic theory) we estimate for cumulene a second sound velocity in the range of 2.4-3.2 km s-1.

A major issue in the development of Lead halide perovskites is the assessment of the crystal structure of the samples, due to their typically limited time-stability, and the understanding of the role of external factors that can induce a crystal phase transformation (such as humidity, intense light flux, temperature, etc.). In this perspective, it is of utmost importance to have at disposal a fast and reliable experimental tool able to give an immediate indication of the polymorph of the sample with the possibility to integrate in-situ measurements for constant monitoring. In this paper we propose Raman spectroscopy as the ideal technique to solve this problem. The vibrational analysis of CsPbI3 in the α-phase and δ-phase and of the Cs4PbI6 secondary phase is reported and all the vibrational modes are assigned by comparing experimental spectra of the phases to Raman modes calculated within the DFT framework. Finally, the mechanism of laser induced phase degradation was studied using in-situ Raman measurements providing new insights on the secondary phase generated during the process.

By combining electron microscopy measurements, atomistic simulations and elastic homogenization theory, we theoretically investigate the Young’s modulus of nanoporous Au structures. Based on atomistic replicas generated starting from experimental tomographic evidence, atomistic simulations reveal that nanoporous Au stiffens as ligaments become finer, reproducing experimental findings obtained by nanoindentation of dealloyed samples. We argue that such a stiffening is neither due to surface stress nor to grain boundaries. Instead, we observe a direct quantitative correlation between the density of dislocations found in the material phase of the nanoporous structures and their Young’s modulus and we propose a microscopic explanation of the observed stiffening. In particular, we show that local stress and strain fields in the neighborhood of dislocation cores allow dislocations to work as reinforcing solutes.

Cluster-assembled metallic films show interesting electrical properties, both in the near-to-percolation regime, when deposited clusters do not form a complete layer yet, and when the film thickness is well above the electrical percolation threshold. Correctly estimating their electrical conductivity is crucial, but, particularly for the latter regime, standard theoretical tools are not quite adequate. We therefore developed a procedure based on an atomically informed mesoscopic model in which ab-initio estimates of electronic transport at the nanoscale are used to reconstruct the conductivity of nanogranular gold films generated by molecular dynamics. An equivalent resistor network is developed, appropriately accounting for ballistic transport. The method is shown to correctly capture the non-monotonic behavior of the conductivity as a function of the film thickness, namely a signature feature of nanogranular films.

Thermal conductivity of bulk Si0.5 Ge0.5 at room temperature has been calculated using density functional perturbation theory and the phonon Boltzmann transport equation. Within the virtual crystal approximation, second- and third-order interatomic force constants have been calculated to obtain anharmonic phonon scattering terms. An additional scattering term is introduced to account for mass disorder in the alloy. In the same way, mass disorder resulting from n- and p-type dopants with different concentrations has been included, considering doping with III-group elements (p-type) such as B, Al, and Ga, and with V-group elements (n-type) such as N, P, and As. Little effect on the thermal conductivity is observed for all dopants with a concentration below 1021 cm−3. At higher concentration, reduction by up to 50% is instead observed with B-doping in agreement with the highest mass variance. Interestingly, the thermal conductivity even increases with respect to the pristine value for dopants Ga and As. This results from a decrease in the mass variance in the doped alloy, which can be considered a ternary system. Results are compared to the analogous effect on the thermal conductivity in doped Si.

Second sound is known as the thermal transport regime where heat is carried by temperature waves. Its experimental observation was previously restricted to a small number of materials, usually in rather narrow temperature windows. We show that it is possible to overcome these limitations by driving the system with a rapidly varying temperature field. High-frequency second sound is demonstrated in bulk natural Ge between 7 K and room temperature by studying the phase lag of the thermal response under a harmonic high-frequency external thermal excitation and addressing the relaxation time and the propagation velocity of the heat waves. These results provide a route to investigate the potential of wave-like heat transport in almost any material, opening opportunities to control heat through its oscillatory nature., We acknowledge financial support from the Spanish Ministry of Economy, Industry, and Competitiveness through the “Severo Ochoa” Program for Centers of Excellence in R&D (SEV-2015-0496 and CEX2019-000917-S), MAT2017-90024-P (TANGENTS)-EI/FEDER, 2020AEP141, grant no. RTI2018-097876-B-C22 (MCIU/AEI/FEDER, UE), and the Generalitat de Catalunya under grant nos. 2017-SGR-1506 and 2017-SGR-00488. We thank the Centro de Supercomputación de Galicia (CESGA) for the use of their computational resources. M.L.-S. was funded through the Juan de la Cierva programme.

Funder: Consortium des Équipements de Calcul Intensif, Funder: The Leverhulme Trust, While the charge transport properties of organic semiconductors have been extensively studied over the recent years, the field of organics‐based thermoelectrics is still limited by a lack of experimental data on thermal transport and of understanding of the associated structure–property relationships. To fill this gap, a comprehensive experimental and theoretical investigation of the lattice thermal conductivity in polycrystalline thin films of dinaphtho[2,3‐b:2′,3′‐f]thieno[3,2‐b]thiophene (Cn‐DNTT‐Cn with n = 0, 8) semiconductors is reported. Strikingly, thermal conductivity appears to be much more isotropic than charge transport, which is confined to the 2D molecular layers. A direct comparison between experimental measurements (3ω–Völklein method) and theoretical estimations (approach‐to‐equilibrium molecular dynamics (AEMD) method) indicates that the in‐plane thermal conductivity is strongly reduced in the presence of the long terminal alkyl chains. This evolution can be rationalized by the strong localization of the intermolecular vibrational modes in C8‐DNTT‐C8 in comparison to unsubstituted DNTT cores, as evidenced by a vibrational mode analysis. Combined with the enhanced charge transport properties of alkylated DNTT systems, this opens the possibility to decouple electron and phonon transport in these materials, which provides great potential for enhancing the thermoelectric figure of merit ZT.

A systematic study based on state-of-the-art first-principles calculations has been carried out to determine intrinsic thermoelectric properties in $n$- and $p$-type SiGe alloys. Both electronic and thermal transport coefficients have been evaluated using the Boltzmann transport equation, applied on the electronic and phonon band structure, respectively. The Seebeck coefficient, electrical conductivity, and thermal conductivity have been analyzed focusing on the effect of carrier concentration, temperature, and alloy composition. The resulting figure of merit is highest for heavy doping and at elevated temperatures ($g$1000 K) in the SiGe alloy with Ge content from 50% to 80%.

The development of new luminescent materials for lighting applications or stress sensors, mechano-driven lighting devices is a crucial technological topic. Materials suitable for these applications should guarantee a high chemical stability, easiness and green sintering procedure and optimal optical properties. In this framework Calcium Zinc oxysulfide (CaZnOS) represents one of the most promising materials, for its near UV excitation with a broad visible emission, a long phosphorescence and a mechano-luminescence effect that still need to be explored. In this work we report the optical properties and the kinetics of radiative recombination upon intrinsic and extrinsic excitation of pure CaZnOS, assessing the vibrational properties by means of Raman spectroscopy, and corroborated by DFT calculations. The analysis of time resolved measurements at room and low temperature (up to 10 K) give new insight on the distribution and nature of the defects that generate the luminescence upon external stress as well the long phosphorescence. Herein, we also present a model of the intrinsic defects and on the energy transfer mechanism among levels in pure CaZnOS matrix, opening new perspectives also on doped materials and for the development of piezoluminescent devices.

In this work we study the effect of different synthetic conditions on thermal transport properties of poly(3,4-ethylenedioxythiophene) (PEDOT) by focusing in particular on the role of proton scavengers. To this aim, different PEDOT samples were generated in silico using a novel computational algorithm based on a combination of first-principles density functional theory and classical molecular dynamics simulations. The corresponding thermal conductivities were then estimated using the approach to equilibrium molecular dynamics methodology. The results show that the initial synthetic conditions strongly affect the corresponding thermal conductivities, which display variations up to a factor of $\ensuremath{\sim}2$ depending on the proton scavenger. By decomposing the thermal conductivity tensor along the direction of maximum chain alignment and the corresponding perpendicular directions, we attribute the thermal conductivity differences to the variations in the average polymer chain length ${\ensuremath{\lambda}}_{\mathrm{ave}}$. A dependence of the thermal conductivity with the polydispersity index was finally observed, suggesting a possible role of intercrystallite chains in enhancing thermal transport properties. By means of the Green-Kubo modal analysis, we eventually characterize the vibrational modes involved in PEDOT thermal transport and investigate how they are related to the thermal conductivity values of the samples.

The study of new phosphors requires in-depth knowledge of the mechanisms and radiative emission paths and, with this aim, the study here reported focuses on the emission properties of CaZnOS crystals single doped with Terbium and co-doped with Terbium and Europium. By studying the optical properties and, in particular, the kinetics of recombination with time-resolved luminescence, the de-excitation mechanisms and the charge transfer processes have been established. A fundamental role is played by the defective centers and their efficient energy transfer process to the excited levels of Terbium, the mechanism being also active among co-doping rare earths (from Tb3+ to Eu3+), allowing further tuning of the emission properties. Beside photoluminescence, the study shows that in case of mechanical stimulus as well, the mechano-luminescence follows the same path, where the defective states of the matrix efficiently excite the levels of dopants, producing a green emission at 545 nm from Tb3+ and a red emission above 600 nm from Eu3+. Therefore, studying the relative ratio of dopants, it is shown how precisely tune across the visible part of the spectrum the mechano-luminescence emission.

The validity of Fourier’s law in telescopic nanowires is tested by means of molecular dynamics simulations. We observe that the radial dependence of the heat-flux profile, the temperature jump, and the appearance of vorticity obtained in molecular dynamics telescopic wires near the contact point acquire a hydrodynamic character, and we show that they are incompatible with Fourier’s law. We propose the Guyer-Krumhansl equation as a generalization capable of capturing these hydrodynamic effects. Lattice-dynamics results show that the thermal average of the confined modes shows no radial dependence of the vibrating energy inside the wire. This means that hydrodynamic effects could not be related to the confinement effects in these small systems.

Pentameric ligand-gated ion channels are an important class of widely expressed membrane neuroreceptors, which play a crucial role in fast synaptic communications and are involved in several neurological conditions. They are activated by the binding of neurotransmitters, which trigger the transmission of an electrical signal via facilitated ion-flux. They can also be activated, inhibited or modulated by a number of drugs. Mutagenesis electrophysiology experiments, with natural or unnatural amino acids, have provided a large body of functional data that, together with emerging structural information from X-ray spectroscopy and cryo-electron microscopy, are helping unravel the complex working mechanisms of these neuroreceptors. Computer simulations are complementing these mutagenesis experiments, with insights at various levels of accuracy and resolution. Here we review how a selection of computational tools, including first principles methods, classical molecular dynamics and enhanced sampling techniques, are contributing to construct a picture of how pentameric ligand-gated ion channels function and can be pharmacologically targeted to treat the disorders they are responsible for.

Micromorphology of conjugated polymers is expected to play a crucial role in both heat and charge transport properties. In this perspective, the details of the polymerization mechanism acquire a fundamental relevance, providing the link between the basic chemical reaction paths and the resulting molecular structure and arrangement. For PEDOT, the role played by the Bronsted bases (proton scavengers) and their impact on the distribution of polymer chain lengths are still a matter of debate. In the present work, we have systematically analyzed several reaction paths leading to PEDOT polymerization. By means of atomistic simulations, we identified the thermodynamically preferred reaction path, proving that tosylate anions rule proton scavenging. PEDOT chain length was computed to be ∼12-13 monomeric units. We could also demonstrate how the proton scavengers set at once the chain lengths and the sample crystallinity. Furthermore, we found that tosylate gives rise to a sharper multimodal distribution of chain length, a feature that supports hypotheses regarding the occurrence of a percolative transport regime mediated by tie chains bridging paracrystalline regions.

Using a combination of equilibrium classical molecular dynamics (within the Green-Kubo formalism) and the Boltzmann transport equation, we study the effect of strain on the ZnO thermal conductivity focusing in particular on the case of hydrostatic and uniaxial strain. The results show that in the case of hydrostatic strain up to ± 4 % , we can obtain thermal conductivity variations of more than 100%, while for uniaxial strains the calculated thermal conductivity variations are comparatively less pronounced. In particular, by imposing uniaxial compressive strains up to − 4 % , we estimate a corresponding thermal conductivity variation close to zero. The mode analysis based on the solution of the Boltzmann transport equation shows that for hydrostatic strains, the thermal conductivity variations are mainly due to a corresponding modification of the phonon relaxations times. Finally, we provide evidence that for uniaxial compressive strains the contribution of the phonon relaxations time is balanced by the increase of the group velocities leading to a thermal conductivity almost unaffected by strain.

We critically address the problem of predicting the thermal boundary resistance at the interface between two semiconductors by atomistic simulations. After reviewing the available models, lattice dynamics calculations and molecular dynamics simulation protocols, we reformulate this problem in the language of non-equilibrium thermodynamics, providing an elegant, robust and valuable theoretical framework for the direct calculation of the thermal boundary resistance through molecular dynamics simulations. The foundation of the method, as well as its subtleties and the details of its actual implementation are presented. Finally, the Si/Ge interface showcase is discussed as the prototypical example of semiconductor heterojunction whose thermal properties are paramount in many front-edge nanotechnologies.

Two different methods have been applied to create differently structured nanocrystalline graphene samples used in molecular dynamics simulations. In the first method, graphene sheets are generated by grain growth from individual nucleation seeds. The second method applies Voronoi tessellation to define single crystalline domains in the simulation cells. The differently generated nanocrystalline graphene sheets show significant variations in the grain size distribution and the shape of the crystalline domains. Furthermore, out-of-plane corrugation is found to be more pronounced in samples generated by the Voronoi method, in particular for small grain sizes (≤14 nm). Marginal differences are observed in the distribution of polygonal rings in the grain boundaries which might result from the geometrical shape of the grain boundaries. Thermal conductivity has been determined using the approach-to-equilibrium molecular dynamics formalism. A lower thermal conductivity is observed in Voronoi samples for grain siz...

Poly(3,4-ethylenedioxythiophene) (PEDOT) polymerization has been carried out both in a template-free environment and inside the nanopores of SBA-15 mesoporous silica. Comparing the two methods and the secondary doping of commercial PEDOT:PSS, we were able to study the structural effect of the templated polymerization via a multi-technique approach. We found that the confined polymerization favours a more linear configuration of the polymer chains, in a similar way to the well-known secondary doping with organic solvents. Moreover, comparison of computational and experimental results suggests that the PEDOT mean chain length is greater when the polymerization occurs in the nanoporous template, promoting the formation of a polymer with larger molecular weight and crystallinity.

We present a computational investigation on heat transport in a single polymer chain of poly-3,4-ethylenedioxythiophene (PEDOT). By applying equilibrium and nonequilibrium molecular dynamics simulations to evaluate the thermal conductivity, as well as by investigating how the polymer chain approaches equilibrium upon a local thermal excitation, we provide a robust picture assessing the anomalous superdiffusive (i.e., intermediate between ballistic and diffusive) character of its thermal transport. This assessment is provided by the present simulations showing that three scaling laws with unlike physical meaning and characterizing the thermal energy transport in one-dimensional systems indeed occur in the very same polymer chain with consistent critical exponents. In order to disentangle the effect of dimensionality, we perform a systematic comparison of transport features for a single one-dimensional (1D) PEDOT chain and a three-dimensional (3D) PEDOT crystal. Present simulations suggest that by increasing the dimensionality, the anomalous regime is completely removed as due to the occurrence of strong interchains anharmonic interactions. Finally, we prove that thermal transport in isolated single PEDOT chains belongs to a novel universality class of superdiffusion characterized by a critical exponent $\ensuremath{\beta}=1/2$.

We present and discuss a computational setup aimed at modeling the polymerization process of eumelanin by combining together molecular dynamics simulations and ab initio total-energy calculations. By simulating the oxidative polymerization process of eumelanin in methanol, we provide evidence that “in silico” synthesized samples are mostly composed of low-molecular-weight structures: an exponential distribution of the molecular weights is found, yielding an average weight less than 10. Adopting the scheme of chemical disorder, we also perform a statistical analysis on the variety of molecules formed, focusing on both their structural and electronic features. In particular, we identify the most frequent structural patterns within the molecules by analyzing the occurrence of the single chemical bonds. Moreover, we show how most of the molecules have a large number of nonterminated oxygen atoms, highlighting the pivotal role of =O groups in the eumelanin molecular stability., We acknowledge the Regione Sardegna basic research Project no. CRP78744 “Energy Applications with Porous Silicon (ENAPSi).” E.C. acknowledges support from MINECO (Spain) (Grant FIS2015-64886-C5-4-P), the Severo Ochoa Centers of Excellence Program (Grant SEV-2015-0496), and Generalitat de Catalunya (2017SGR1506).

The organic/inorganic interface in thin nanosized porous structures has a key role in determining the final properties of the composite materials. By use of the porous silicon/eumelanin hybrids as a case study, the role of this interface was investigated by experimental and computational methods. Our results show that an increased polymer density close to the hybrid interface strongly modifies the diffusion of the chemical species within the polymer molecule, affecting then the oxidation level of the pores' inner Si surface. We observed a greater stability induced by increased pore diameter, a behavior that with computational and chemical arguments we attributed to a modified diffusion of the hydrogen peroxide toward the Si/eumelanin interface. Our results show that the overall behavior of a polymer when inserted in a tiny nanoscale structure must be taken into account for a correct understanding and control of the hybrids properties and that the formation of the interface alone may not be sufficient. © 2018 American Chemical Society.

Ideal thermoelectric materials should possess low thermal conductivity $$\kappa $$ along with high electrical conductivity $$\sigma $$ . Thus, strategies are needed to impede the propagation of phonons mostly responsible for thermal conduction while only marginally affecting charge carrier diffusion. Defect engineering may provide tools to fulfill this aim, provided that one can achieve an adequate understanding of the role played by multiple morphological defects in scattering thermal energy carriers. In this paper, we study how various morphological defects such as grain boundaries and dispersed nanovoids reduce the thermal conductivity of silicon. A blended approach has been adopted, using data from both simulations and experiments in order to cover a wide range of defect densities. We show that the co-presence of morphological defects with different characteristic scattering length scales is effective in reducing the thermal conductivity. We also point out that non-gray models (i.e. models with spectral resolution) are required to improve the accuracy of predictive models explaining the dependence of $$\kappa $$ on the density of morphological defects. Finally, the application of spectral models to Matthiessen’s rule is critically addressed with the aim of arriving at a compact model of phonon scattering in highly defective materials showing that non-local descriptors would be needed to account for lattice distortion due to nanometric voids.

Pentameric ligand-gated ion channels (pLGICs) are important biomolecules that mediate fast synaptic transmission. Their malfunctions are linked to serious neuronal disorders and they are major pharmaceutical targets; in invertebrates, they are involved in insecticide resistance. The complexity of pLGICs and the limited crystallographic information available prevent a detailed understanding of how they function. State-of-the-art computational techniques are therefore crucial to build an accurate picture at the atomic level of the mechanisms which drive the activation of pLGICs, complementing the available experimental data. We have used a series of simulation methods, including homology modelling, ligand–protein docking, density functional theory, molecular dynamics and metadynamics, a powerful scheme for accelerating rare events, with the guidance of mutagenesis electrophysiology experiments, to explore ligand-binding mechanisms, the effects of mutations and the potential role of a proline molecular switch for the gating of the ion channels. Results for the insect RDL receptor, the GABAC receptor, the 5-HT3 receptor and the nicotinic acetylcholine receptor will be reviewed.

The measurement of the Avogadro constant by counting Si atoms is based on the assumption that Si balls of about 94 mm diameter have a perfect crystal structure up to the outermost atom layers. This is not the case because of the surface relaxation and reconstruction, the possible presence of an amorphous layer, and the oxidation process due to the interaction with the ambient. This paper gives the results of density functional calculations of the strain components orthogonal to crystal surface in a number of configurations likely found in real samples.

We studied thermal conductivity of the three most stable hydrogenated graphene (graphane) conformers by means of non-equilibrium molecular dynamics. We estimated thermal conductivity for pristine graphene with sample length 2.1 (2.4) μm as large as κ = 745.4 ± 0.3 and 819.1 ± 0.3 W m−1 K−1 in the armchair and zigzag directions, respectively, in very good agreement with previous theoretical results based on the Boltzmann transport equation. In the case of the three graphane isomers we observed a dramatic κ reduction by at least one order of magnitude with respect to pristine graphene. We elucidated this reduction in terms of different phonon density of states and mean-free path distribution between graphene and graphane. The deterioration of thermal transport upon hydrogenation in graphene, could be proposed as a way to tune thermal transport in graphene for phononic applications such as thermal diodes.

Among the possible applications of eumelanin (biolelectronics, biointerfaces, etc.), photovoltaics is a promising field which could highly benefit from its intrinsic features (broadband UV–vis absorption, etc.), with such a pigment employed as photoactive layer in hybrid solar cells. The envisioned application poses the need for a careful theoretical analysis on the adhesion properties of eumelanin on a substrate and the characterization of the hybrid system electronic features. In this work, we investigate a eumelanin/Si interface, where Si plays the role of inorganic layer. By means of ab initio calculations, we study the feasibility of the experimental formation process of eumelanin protomolecular structures in methanol ambient, evaluating the corresponding formation energy. Then, we explore the adhesion properties of eumelanin molecules on a silicon surface and extract the electronic structure of the resulting system. The corresponding band alignment is then used to address the overall photoconversion efficiency. Adopting the scheme of chemical disorder, which has been proved to successfully capture the variety of eumelanin protomolecules, we show that (1) the formation process of eumelanin protomolecules from the constituting monomers is generally hindered in a solvent environment with respect to vacuum and (2) key factors in improving the adhesion properties and band lineup of the molecules on an inorganic interface are the molecular electronic state and the planarity of their structures. Protomolecular models with a large number of nonterminated oxygen atoms and endowed with an intrinsically planar character tend to bind more strongly to the surface. In addition, they are more likely to produce a favorable band alignment for photoconversion applications., We acknowledge the Regione Sardegna basic research Project No. CRP78744 “Energy Applications with Porous Silicon (ENAPSi)”. E.C. acknowledges support by MINECO (Spain) through Grant FIS2015-64886-C5-4-P and the Severo Ochoa Centers of Excellence Program (Grant SEV-2015-0496) as well as by Generalitat de Catalunya (2014SGR301).

We introduce a nonequilibrium molecular dynamics simulation approach, based on the generalized Langevin equation, to study vibrational energy relaxation in pump-probe spectroscopy. A colored noise thermostat is used to selectively excite a set of vibrational modes, leaving the other modes nearly unperturbed, to mimic the effect of a monochromatic laser pump. Energy relaxation is probed by analyzing the evolution of the system after excitation in the microcanonical ensemble, thus providing direct information about the energy redistribution paths at the molecular level and their time scale. The method is applied to hydrogen-bonded molecular liquids, specifically deuterated methanol and water, providing a robust picture of energy relaxation at the molecular scale.

Single grain boundaries of crystalline graphene with varying mismatch angles from 3° to 16° have been investigated using molecular dynamics simulations. Four- to eight-atomic rings are found to be the most abundant non-hexagonal polygons in the grain boundary for all mismatch angles. Tetra- and octagons are predominant for mismatch angles of 4.1° and 6.6° in contrast to nanocrystalline samples where penta- and heptagons are dominating. Out-of-plane buckling at the grain boundary is most pronounced for a mismatch angle of 3.0° and it tends to decrease with increasing mismatch angle. At 16.1°, the out-of-plane buckling vanishes. Analysis of the vibrational density of states of boundary atoms revealed a significant decrease of the main peak of optical vibrations and the evolution of secondary peaks below and above the major frequency attributed to vibrations of non-hexagonal rings. The thermal boundary resistance in single graphene interfaces has been approximated. It tends to increase with increasing mismatch angle, indicating reduced thermal conductivity when such interfaces are present in crystalline graphene. In nanocrystalline graphene samples, the thermal conductivity is significantly reduced with respect to crystalline graphene and it decreases with decreasing grain size according to an increasing number of single boundaries.

© 2017 American Chemical Society. Ultrathin metal nanoparticles coatings, synthesized by gas-phase deposition, are emerging as go-to materials in a variety of fields ranging from pathogens control and sensing to energy storage. Predicting their morphology and mechanical properties beyond a trial-and-error approach is a crucial issue limiting their exploitation in real-life applications. The morphology and mechanical properties of Ag nanoparticle ultrathin films, synthesized by supersonic cluster beam deposition, are here assessed adopting a bottom-up, multitechnique approach. A virtual film model is proposed merging high resolution scanning transmission electron microscopy, supersonic cluster beam dynamics, and molecular dynamics simulations. The model is validated against mechanical nanometrology measurements and is readily extendable to metals other than Ag. The virtual film is shown to be a flexible and reliable predictive tool to access morphology-dependent properties such as mesoscale gas-dynamics and elasticity of ultrathin films synthesized by gas-phase deposition. ispartof: Journal of Physical Chemistry C vol:121 issue:40 pages:22434-22441 status: published

The Thermal Boundary Resistance at the interface between a nanosized Al film and an Al_{2}O_{3} substrate is investigated at an atomistic level. A room temperature value of 1.4 m^{2}K/GW is found. The thermal dynamics occurring in time-resolved thermo-reflectance experiments is then modelled via macro-physics equations upon insertion of the materials parameters obtained from atomistic simulations. Electrons and phonons non-equilibrium and spatio-temporal temperatures inhomo- geneities are found to persist up to the nanosecond time scale. These results question the validity of the commonly adopted lumped thermal capacitance model in interpreting transient nanocalorimetry experiments. The strategy adopted in the literature to extract the Thermal Boundary Resistance from transient reflectivity traces is revised at the light of the present findings. The results are of relevance beyond the specific system, the physical picture being general and readily extendable to other heterojunctions., 12 pages, 8 figures

Inspired by pulsed laser-assisted thermal relaxation experiments, we simulated the response of a nanometer-size monolayer graphene sample to thermal impulses by means of nonequilibrium molecular dynamics. By following the time evolution of the temperature profile until equilibrium is eventually reached, we obtain a direct estimation of the thermal conductivity of the excited graphene sample. It is shown that the predicted thermal conductivity depends on which vibrational degrees of freedom are in fact excited by the thermal impulse, suggesting that its determination depends, among many other issues, on the actual phonon population generated in the sample. The situation here explored is typically found in experiments or simulations addressing a transient regime of approach to equilibrium.

By using state-of-the-art atomistic methods we provide an accurate estimate of thermal conductivity of methylammonium lead halide as a function of sample size and temperature, in agreement with experimental works. We show that the thermal conductivity of methylammonium lead halide is intrinsically low, due to the low sound velocity of the PbI lattice. Furthermore, by selectively analyzing the effect of different molecular degrees of freedom, we clarify the role of the molecular substructure by showing that the internal modes above 150 cm(-1) (in addition to rotations) are effective in reducing the thermal conductivity of hybrid perovskites. This analysis suggests strategies to tailor the thermal conductivity by modifying the internal structure of organic cations.

We describe a test carried out by using a two-thickness interferometer to investigate the effect of the surface stress on the measurement of the silicon lattice constant.

We discuss about computer experiments based on nonequilibrium molecular dynamics simulations providing evidence that thermal rectification can be obtained in bulk Si by a non-uniform distribution of defects. We consider a graded population of both Ge substitutional defects and nanovoids, distributed along the direction of an applied thermal bias, and predict a rectification factor comparable to what is observed in other low–dimensional Si–based nanostructures. By considering several defect distribution profiles, thermal bias conditions, and sample sizes, the present results suggest that a possible way for tuning the thermal rectification is by defect engineering., We acknowledge the financial support by the Spanish MINECO under Grant Nos. FEDER-FIS2012-37549-C05-02, FEDER-MAT2013-40581-P, TEC2012-31330, and TEC2015-67462-C2-1-R, the Generalitat de Catalunya under Grant Nos. 2014 SGR 301 and 2014 SGR 384, and the Spanish MINECO through the Severo Ochoa Centres of Excellence Program under Grant Nos. SEV-2013-0295 and SEV-2015-0496. We also acknowledge the financial support by the Regione Sardegna basic research project CRP78744 “Energy Applications with Porous Silicon (ENAPSi).” One of us (R.D.) acknowledges Regione Sardegna for the financial support under project P.O.R. Sardegna F.S.E. 2007-2013 (Axis IV Human Resources, Objective l.3, Line of Activity l.3.1.). We finally acknowledge the computational support by CINECA under ISCRA project TREWI.

Zinc oxide is typically used as an electron acceptor in the preparation of hybrid solar cells. Such hybrids are, in many cases, synthesized from solutions. In this work, we investigate the possible...

We present a molecular dynamics study providing evidence that it is possible to conceive efficient thermal diodes by a suitable hydrogen decoration of graphene nanoribbons. We estimate thermal rectifications at graphane/graphene interfaces with vertical, triangular, and T-shaped morphologies, and we report a significant thermal rectification up to $\ensuremath{\sim}54%$ for the triangular one. The dependence of the thermal rectification on the nanoribbon dimensions, vertex angle, and temperature gradient is also explored. The physical origin of the observed rectification is analyzed in terms of the different temperature dependence of the thermal conductivity in the pristine materials and the overlap of phonon densities in the different morphologies. Finally, we propose an effective continuum model to describe thermal rectification, which is only based on the steady state temperature profile rather than the actual heat flux. The model quantitatively predicts thermal rectification in very good agreement with the standard analysis based on the heat flux estimate.

We study the adhesion and the diffusion of single zinc-phthalocyanine (ZnPc) molecules on a ZnO (1010) surface by means of model potential molecular dynamics. We find that the molecule is easily adsorbed on the surface, and we identify the ZnPc adsorption sites. The diffusion at room temperature is studied by metadynamics. We find that the molecule is able to diffuse by hopping between the surface dimer rows along the [010] crystallographic direction with a free energy barrier as small as ∼0.4 eV. At temperatures T > 700 K, a different mechanism is found with large diffusion paths along the surface trench grooves.

By means of large-scale atomistic simulations, we investigate theoretically the interface between poly(3-hexylthiophene) (P3HT) and zinc oxide. We observe a spontaneous tendency of the polymer to disorder close to the surface, and we attribute such a result to lattice spacing mismatch. By using simple effective models, we calculate the maximum polymer mobility normal to the surface that turns out to be strongly affected by the disorder at the interface. According to the present analysis, we propose that modifications of the polymer and the lattice parameter of the inorganic substrate could improve the overall transport properties at the interface.

The rat α7 nicotinic acetylcholine receptor (nAChR) has a proline residue near the middle of the β9 strand. The replacement of this proline residue at position 180 (P180) by either threonine (α7-P180T) or serine (α7-P180S) slowed the onset of desensitization dramatically, with half-times of ∼930 and 700 ms, respectively, compared to 90 ms for the wild-type receptor. To investigate the importance of the hydroxyl group on the position 180 side-chains, the mutant receptors α7-P180Y and α7-P180F were studied and showed half-times of desensitization of 650 and 160 ms, respectively. While a position 180 side-chain OH group may contribute to the slow desensitization rates, α7-P180S and α7-P180V resulted in receptors with similar desensitization rates, suggesting that increased backbone to backbone H bonding expected in the absence of proline at position 180 would likely exert a great effect on desensitization. Single channel recordings indicated that for the α7-P180T receptor there was a significantly reduced closed time without any change in single channel conductance (as compared to wild-type). Kinetic simulations indicated that all changes observed for the mutant channel behaviour were reproduced by decreasing the rate of desensitization, and increasing the microscopic affinity to resting receptors. Molecular dynamics (MD) simulations on a homology model were used to provide insight into likely H bond interactions within the outer β-sheet that occur when the P180 residue is mutated. All mutations analysed increased about twofold the predicted number of H bonds between the residue at position 180 and the backbone of the β10 strand. Moreover, the α7-P180T and α7-P180S mutations also formed some intrastrand H bonds along the β9 strand, although H bonding of the OH groups of the threonine or serine side-chains was predicted to be infrequent. Our results indicate that rapid desensitization of the wild-type rat α7 nAChR is facilitated by the presence of the proline residue within the β9 strand.