Atomistic near-field nanoplasmonics: reaching atomic-scale resolution in nanooptics.

Electromagnetic field localization in nanoantennas is one of the leitmotivs that drives the development of plasmonics. The near-fields in these plasmonic nanoantennas are commonly addressed theoretically within classical frameworks that neglect atomic-scale features. This approach is often appropriate since the irregularities produced at the atomic scale are typically hidden in far-field optical spectroscopies. However, a variety of physical and chemical processes rely on the fine distribution of the local fields at this ultraconfined scale. We use time-dependent density functional theory and perform atomistic quantum mechanical calculations of the optical response of plasmonic nanoparticles, and their dimers, characterized by the presence of crystallographic planes, facets, vertices, and steps. Using sodium clusters as an example, we show that the atomistic details of the nanoparticles morphologies determine the presence of subnanometric near-field hot spots that are further enhanced by the action of the underlying nanometric plasmonic fields. This situation is analogue to a self-similar nanoantenna cascade effect, scaled down to atomic dimensions, and it provides new insights into the limits of field enhancement and confinement, with important implications in the optical resolution of field-enhanced spectroscopies and microscopies.

Spin-dependent electron scattering at graphene edges on Ni(111).

We investigate the scattering of surface electrons by the edges of graphene islands grown on Ni(111). By combining local tunneling spectroscopy and ab initio electronic structure calculations we find that the hybridization between graphene and Ni states results in strongly reflecting graphene edges. Quantum interference patterns formed around the islands reveal a spin-dependent scattering of the Shockley bands of Ni, which we attribute to their distinct coupling to bulk states. Moreover, we find a strong dependence of the scattering amplitude on the atomic structure of the edges, depending on the orbital character and energy of the surface states.

Time-dependent electron phenomena at surfaces.

Femtosecond and subfemtosecond time scales typically rule electron dynamics at metal surfaces. Recent advance in experimental techniques permits now remarkable precision in the description of these processes. In particular, shorter time scales, smaller system sizes, and spin-dependent effects are current targets of interest. In this article, we use state-of-the-art theoretical methods to analyze these refined features of electron dynamics. We show that the screening of localized charges at metal surfaces is created locally in the attosecond time scale, while collective excitations transfer the perturbation to larger distances in longer time scales. We predict that the elastic width of the resonance in excited alkali adsorbates on ferromagnetic surfaces can depend on spin orientation in a counterintuitive way. Finally, we quantitatively evaluate the electron-electron and electron-phonon contributions to the electronic excited states widths in ultrathin metal layers. We conclude that confinement and spin effects are key factors in the behavior of electron dynamics at metal surfaces.

Electronic stopping power in gold: the role of d electrons and the H/He anomaly.

The electronic stopping power of H and He moving through gold is obtained to high accuracy using time-evolving density-functional theory, thereby bringing usual first principles accuracies into this kind of strongly coupled, continuum nonadiabatic processes in condensed matter. The two key unexplained features of what observed experimentally have been reproduced and understood: (i) The nonlinear behavior of stopping power versus velocity is a gradual crossover as excitations tail into the d-electron spectrum; and (ii) the low-velocity H/He anomaly (the relative stopping powers are contrary to established theory) is explained by the substantial involvement of the d electrons in the screening of the projectile even at the lowest velocities where the energy loss is generated by s-like electron-hole pair formation only.

Transport properties of armchair graphene nanoribbon junctions between graphene electrodes.

The transmission properties of armchair graphene nanoribbon junctions between graphene electrodes are investigated by means of first-principles quantum transport calculations. First the dependence of the transmission function on the size of the nanoribbon has been studied. Two regimes are highlighted: for a small applied bias transport takes place via tunneling and the length of the ribbon is the key parameter that determines the junction conductance; at a higher applied bias resonant transport through the HOMO and LUMO starts to play a more determinant role, and the transport properties depend on the details of the geometry (width and length) of the carbon nanoribbon. In the case of the thinnest ribbon it has been verified that a tilted geometry of the central phenyl ring is the most stable configuration. As a consequence of this rotation the conductance decreases due to the misalignment of the π orbitals between the phenyl ring and the remaining part of the junction. All the computed transmission functions have shown a negligible dependence on different saturations and reconstructions of the edges of the graphene leads, suggesting a general validity of the reported results.

Role of dispersion forces in the structure of graphene monolayers on Ru surfaces.

Elaborate density functional theory (DFT) calculations that include the effect of van der Waals (vdW) interactions have been carried out for graphene epitaxially grown on Ru(0001). The calculations predict a reduction of structural corrugation in the observed moiré pattern of about 25% (∼0.4 Å) with respect to DFT calculations without vdW corrections. The simulated STM topographies are close to the experimental ones in a wide range of bias voltage around the Fermi level.

Direct observation of electron dynamics in the attosecond domain.

Dynamical processes are commonly investigated using laser pump-probe experiments, with a pump pulse exciting the system of interest and a second probe pulse tracking its temporal evolution as a function of the delay between the pulses. Because the time resolution attainable in such experiments depends on the temporal definition of the laser pulses, pulse compression to 200 attoseconds (1 as = 10(-18) s) is a promising recent development. These ultrafast pulses have been fully characterized, and used to directly measure light waves and electronic relaxation in free atoms. But attosecond pulses can only be realized in the extreme ultraviolet and X-ray regime; in contrast, the optical laser pulses typically used for experiments on complex systems last several femtoseconds (1 fs = 10(-15) s). Here we monitor the dynamics of ultrafast electron transfer--a process important in photo- and electrochemistry and used in solid-state solar cells, molecular electronics and single-electron devices--on attosecond timescales using core-hole spectroscopy. We push the method, which uses the lifetime of a core electron hole as an internal reference clock for following dynamic processes, into the attosecond regime by focusing on short-lived holes with initial and final states in the same electronic shell. This allows us to show that electron transfer from an adsorbed sulphur atom to a ruthenium surface proceeds in about 320 as.

An O(N3) implementation of Hedin's GW approximation for molecules.

We describe an implementation of Hedin's GW approximation for molecules and clusters, the complexity of which scales as O(N(3)) with the number of atoms. Our method is guided by two strategies: (i) to respect the locality of the underlying electronic interactions and (ii) to avoid the singularities of Green's functions by manipulating, instead, their spectral functions using fast Fourier transform methods. To take into account the locality of the electronic interactions, we use a local basis of atomic orbitals and, also, a local basis in the space of their products. We further compress the screened Coulomb interaction into a space of lower dimensions for speed and to reduce memory requirements. The improved scaling of our method with respect to most of the published methodologies should facilitate GW calculations for large systems. Our implementation is intended as a step forward towards the goal of predicting, prior to their synthesis, the ionization energies and electron affinities of the large molecules that serve as constituents of organic semiconductors.

Potential energy landscape for hot electrons in periodically nanostructured graphene.

We explore the spatial variations of the unoccupied electronic states of graphene epitaxially grown on Ru(0001) and observed three unexpected features: the first graphene image state is split in energy; unlike all other image states, the split state does not follow the local work function modulation, and a new interfacial state at +3 eV appears on some areas of the surface. First-principles calculations explain the observations and permit us to conclude that the system behaves as a self-organized periodic array of quantum dots.

L3 skeletal muscle index (L3SMI) is a surrogate marker of sarcopenia and frailty in non-small cell lung cancer patients.

Background: Non-small cell lung cancer (NSCLC) is a common and highly lethal disease. As advanced treatment modalities are being developed, improved prognostication methods are sought. L3 skeletal muscle index (L3SMI) and alanine aminotransferase (ALT) levels are accepted surrogate markers of sarcopenia and related frailty. We aimed to evaluate the potential association of these markers with NSCLC patients' survival. Methods: A retrospective, single-center study of an NSCLC patients' cohort. L3SMI was calculated based on skeletal muscle area on computed tomography scans at the level of the L3 vertebra. Clinical data were extracted from clinical charts. Results: A total of 140 patients (56.4% males, median age 66 [range 37-86]) were included in this study, 32% were diagnosed at stage 3 and 45% at stage 4. During the follow-up duration (median of 1.9 years; range 1 month to 6.4 years), 102 patients (72.8%) died. Patients' characteristics that were found to be associated with increased mortality were performance status, albumin and tumor stage at diagnosis. Sarcopenia, defined as low L3SMI (lower than 41 cm2/m2 for women and lower than 53 cm2/m2 for men) was significantly associated with higher risk of mortality compared with patients with normal L3SMI values (77.2%, vs 64.6%, p=0.013) in univariate analysis, but not in a multiple regression analysis. Conclusion: Low L3SMI could serve as a surrogate marker for sarcopenia and frailty and, as such, facilitate the prognostication process of NSCLC patients.

The SIESTA method; developments and applicability.

Recent developments in and around the SIESTA method of first-principles simulation of condensed matter are described and reviewed, with emphasis on (i) the applicability of the method for large and varied systems, (ii) efficient basis sets for the standards of accuracy of density-functional methods, (iii) new implementations, and (iv) extensions beyond ground-state calculations.

On the mechanical and electronic properties of thiolated gold nanocrystals.

We present a quantitative exploration, combining experiment and simulation, of the mechanical and electronic properties, as well as the modifications induced by an alkylthiolated coating, at the single nanoparticle (NP) level. We determined the response of the NPs to external pressure in a controlled manner using an atomic force microscope tip. We found a strong reduction in their Young's modulus, as compared to bulk gold, and a significant influence of strain on the electronic properties of the alkylthiolated NPs. Electron transport measurements of tiny molecular junctions (NP/alkylthiol/CAFM tip) show that the effective tunnelling barrier through the adsorbed monolayer strongly decreases by increasing the applied load, which translates in a remarkable and unprecedented increase in the tunnel current. These observations are successfully explained using simulations based on the finite element analysis (FEA) and first-principles calculations that permit one to consider the coupling between the mechanical response of the system and the electric dipole variations at the interface.

Bioactive sesquiterpenes from Santolina rosmarinifolia subsp. Canescens. A conformational analysis of the germacrane ring.

The hexane extract of aerial parts of Santolina rosmarinifolia subsp. canescens afforded eight new sesquiterpenes in addition to known compounds. Their structures were determined by spectroscopic methods and chemical transformations. The conformational analysis of the germacrane constituents was carried out by spectroscopic methods, including NMR at varying temperature and by molecular mechanics calculations. The antifeedant, antibacterial and antitumoral activity of selected compounds has been tested.

Exploring the tilt-angle dependence of electron tunneling across molecular junctions of self-assembled alkanethiols.

Electronic transport mechanisms in molecular junctions are investigated by a combination of first-principles calculations and current-voltage measurements of several well-characterized structures. We study self-assembled layers of alkanethiols grown on Au(111) and form tunnel junctions by contacting the molecular layers with the tip of a conductive force microscope. Measurements done under low-load conditions permit us to obtain reliable tilt-angle and molecular length dependencies of the low-bias conductance through the alkanethiol layers. The observed dependence on tilt-angle is stronger for the longer molecular chains. Our calculations confirm the observed trends and explain them as a result of two mechanisms, namely, a previously proposed intermolecular tunneling enhancement as well as a hitherto overlooked tilt-dependent molecular gate effect.

Electronic stopping power in LiF from first principles.

Using time-dependent density-functional theory we calculate from first principles the rate of energy transfer from a moving proton or antiproton to the electrons of an insulating material, LiF. The behavior of the electronic stopping power versus projectile velocity displays an effective threshold velocity of approximately 0.2 a.u. for the proton, consistent with recent experimental observations, and also for the antiproton. The calculated proton/antiproton stopping-power ratio is approximately 2.4 at velocities slightly above the threshold (v approximately 0.4 a.u.), as compared to the experimental value of 2.1. The projectile energy loss mechanism is observed to be extremely local.

Ultrafast charge transfer and atomic orbital polarization.

The role of orbital polarization for ultrafast charge transfer between an atomic adsorbate and a substrate is explored. Core hole clock spectroscopy with linearly polarized x-ray radiation allows to selectively excite adsorbate resonance states with defined spatial orientation relative to the substrate surface. For c(4 x 2)S/Ru(0001) the charge transfer times between the sulfur 2s(-1)3p*+1 antibonding resonance and the ruthenium substrate have been studied, with the 2s electron excited into the 3p perpendicular* state along the surface normal and the 3p parallel* state in the surface plane. The charge transfer times are determined as 0.18+/-0.07 and 0.84+/-0.23 fs, respectively. This variation is the direct consequence of the different adsorbate-substrate orbital overlap.

Silicate chain formation in the nanostructure of cement-based materials.

Cement-based materials are ubiquitous in almost all built environment. In spite of this, little is known about the formation and the role played by the silicate chains always present in the cement nanostructure. By means of first principles simulations we provide compelling evidence on the pivotal role played by certain ionic species in the formation of the silicate chains inside the cementitious matrix. Moreover, we corroborate the experimental evidence which shows that the length of the most stable chains with m Si atoms follows a magic-number sequence: m = 3n-1 with n = 1,2,... Our results have been applied in the development of new higher performance cement-based materials by adding nanosilica.

Epstein-Barr nuclear antigen leader protein coactivates transcription through interaction with histone deacetylase 4.

Epstein-Barr nuclear antigen (EBNA) leader protein (EBNALP) coactivates promoters with EBNA2 and is important for Epstein-Barr virus immortalization of B cells. Investigation of the role of histone deacetylases (HDACs) in EBNALP and EBNA2 promoter regulation has now identified EBNALP and EBNA2 to be associated with HDAC4 in a lymphoblastoid cell line. Furthermore, a transcription-deficient EBNALP point mutant did not associate with HDAC4. HDAC4 and 5 overexpression repressed EBNA2 activation and EBNALP coactivation, whereas other HDACs had little effect. Moreover, EBNALP expression decreased nuclear HDAC4. Expression of 14-3-3 anchors HDAC4 in the cytoplasm, increased EBNALP effects, and reversed HDAC4 or 5 repression. HDAC4 reversal depended on the HDAC4 nuclear export sequence. Consistent with EBNALP coactivation being mediated by nuclear HDAC4 depletion, HDAC4 overexpression increased nuclear HDAC4 and specifically repressed EBNA2-dependent activation as well as EBNALP-dependent coactivation. Also, EBNALP, HDAC4, and 14-3-3 could be immunoprecipitated in a single complex. Thus, these data strongly support a model in which EBNALP coactivates transcription by relocalizing HDAC4 and 5 from EBNA2 activated promoters to the cytoplasm. The observed EBNALP effects are likely also in part through HDAC5, which is highly homologous to HDAC4.