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Manjavacas A.,CSIC - Institute of Physical Chemistry "Rocasolano" | Garcia de Abajo F.J.,Catalan Institution for Research and Advanced Studies
Nature communications | Year: 2014

The ability to modulate light at high speeds is of paramount importance for telecommunications, information processing and medical imaging technologies. This has stimulated intense efforts to master optoelectronic switching at visible and near-infrared frequencies, although coping with current computer speeds in integrated architectures still remains a major challenge. As a partial success, mid-infrared light modulation has been recently achieved through gating patterned graphene. Here we show that atomically thin noble metal nanoislands can extend optical modulation to the visible and near-infrared spectral range. We find plasmons in thin metal nanodisks to produce similar absorption cross-sections as spherical particles of the same diameter. Using realistic levels of electrical doping, plasmons are shifted by about half their width, thus leading to a factor-of-two change in light absorption. These results, which we substantiate on microscopic quantum theory of the optical response, hold great potential for the development of electrical visible and near-infrared light modulation in integrable, nanoscale devices.

Cuesta A.,CSIC - Institute of Physical Chemistry "Rocasolano"
ChemPhysChem | Year: 2011

During an electrocatalytic reaction bonds are broken and formed, and this requires that the reactants, the intermediates formed at the elementary reaction steps, and the products interact with a given number of surface atoms of the catalyst. Modifying the number of groups with an adequate number of surface atoms in a suitable geometric arrangement for a determined reaction step to proceed may affect the activity and/or selectivity of the catalyst. Although separating purely geometric atomic ensemble effects from electronic effects is not straightforward, the insights extracted from a detailed investigation of atomic ensemble effects can have a profound impact in the determination of electrocatalytic reaction mechanisms and in the design of more active and more selective electrocatalysts. This Minireview illustrates, using cyanide-modified Pt(111) electrodes as an archetype, how eliminating only one kind of site from the surface (the site-knockout strategy) by means of a regular array of inert adsorbates can be used to successfully study atomic ensemble effects in electrocatalysis. The possible consequences for the design of more efficient and more selective electrocatalysts are also commented on. © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Banos-Sanz J.I.,CSIC - Institute of Physical Chemistry "Rocasolano"
Nucleic acids research | Year: 2013

Uracil-DNA glycosylase (UDG) is a key repair enzyme responsible for removing uracil residues from DNA. Interestingly, UDG is the only enzyme known to be inhibited by two different DNA mimic proteins: p56 encoded by the Bacillus subtilis phage 29 and the well-characterized protein Ugi encoded by the B. subtilis phage PBS1/PBS2. Atomic-resolution crystal structures of the B. subtilis UDG both free and in complex with p56, combined with site-directed mutagenesis analysis, allowed us to identify the key amino acid residues required for enzyme activity, DNA binding and complex formation. An important requirement for complex formation is the recognition carried out by p56 of the protruding Phe191 residue from B. subtilis UDG, whose side-chain is inserted into the DNA minor groove to replace the flipped-out uracil. A comparative analysis of both p56 and Ugi inhibitors enabled us to identify their common and distinctive features. Thereby, our results provide an insight into how two DNA mimic proteins with different structural and biochemical properties are able to specifically block the DNA-binding domain of the same enzyme.

Thongrattanasiri S.,CSIC - Institute of Physical Chemistry "Rocasolano" | Garcia De Abajo F.J.,CSIC - Institute of Physical Chemistry "Rocasolano"
Physical Review Letters | Year: 2013

The ability of plasmons to enhance the electromagnetic field intensity in the gap between metallic nanoparticles derives from their strong optical confinement relative to the light wavelength. The spatial extension of plasmons in doped graphene has recently been shown to be boldly reduced with respect to conventional plasmonic metals. Here, we show that graphene nanostructures are capable of capitalizing such strong confinement to yield unprecedented levels of field enhancement, well beyond what is found in noble metals of similar dimensions (∼ tens of nanometers). We perform realistic, quantum-mechanical calculations of the optical response of graphene dimers formed by nanodisks and nanotriangles, showing a strong sensitivity of the level of enhancement to the type of carbon edges near the gap region, with armchair edges favoring stronger interactions than zigzag edges. Our quantum-mechanical description automatically incorporates nonlocal effects that are absent in classical electromagnetic theory, leading to over an order of magnitude higher enhancement in armchair structures. The classical limit is recovered for large structures. We predict giant levels of light concentration for dimers ∼200 nm, leading to infrared-absorption enhancement factors ∼108. This extreme light enhancement and confinement in nanostructured graphene has great potential for optical sensing and nonlinear devices. © 2013 American Physical Society.

Vegas A.,CSIC - Institute of Physical Chemistry "Rocasolano"
Structure and Bonding | Year: 2011

The study of phase transitions is usually restricted to two to three transformations. Examples of such transitions include the CaF2 → PbCl2 → Ni2In in alloys, the NaCl → CrB → CsCl or the well documented transformation olivine → spinel of the oxides A 2 XO4. These transitions, traditionally regarded as partial processes, have prevented the construction of wider structure maps. One of the scarce examples of these maps was reported by Léger and Haines (Eur J Solid State Inorg Chem 34:785-796, 1997) concerning the phase transitions of AX 2 compounds (dihalides and dioxides), where increasing the coordination number of the A atom is linked to the pressure increase. The structural information, collected in these maps, is always of interest because it limits the number of possible transition paths which may relate a structure-type into another. However, a careful analysis of the partial phase transitions undergone by different compounds, at high temperature and high pressure, reveals that the partial transitions are not isolated processes but they overlap, forming a long, rational pathway that connects all the structures in a coherent manner. Alloys and their related oxides show a similar trend along their concurrent pathways which complement each other. In this work, the analysis is restricted to the AX 2 alloys and their corresponding oxides AX 2 O4, and the results demonstrate that there exists a unifying principle that can be inferred through the simultaneous analysis of all the phase transitions involved in the concurrent structural journeys carried out by both types of compounds. The AX 2 alloys begin the walk in the fluorite-type structure, ending in the MoSi 2-type structure. In the case of the oxides AX 2 O 4, their cation arrays follow a concurrent pathway that, starting at the filled fluorite-type structure, ends in the final Sr2PbO 4-type structure. These structural "journeys" also allows for the discovery of several "missing links" (structure types) which fit into the general sequence and help one understand the whole transitions pathway as a rational process, which takes place simultaneously in the alloys as well as in the cation arrays of the oxides. Very recent works show that alkali metals (Na and K) also join the walk. The extended Zintl-Klemm concept (EZKC) and the concept that relates of oxidation-pressure-temperature effects provide a basis for understanding the observed transitions. © 2011 Springer-Verlag Berlin Heidelberg.

Thongrattanasiri S.,CSIC - Institute of Physical Chemistry "Rocasolano" | Koppens F.H.L.,ICFO - Institute of Photonic Sciences | Garcia De Abajo F.J.,CSIC - Institute of Physical Chemistry "Rocasolano" | Garcia De Abajo F.J.,University of Southampton
Physical Review Letters | Year: 2012

We demonstrate that 100% light absorption can take place in a single patterned sheet of doped graphene. General analysis shows that a planar array of small particles with losses exhibits full absorption under critical-coupling conditions provided the cross section of each individual particle is comparable to the area of the lattice unit cell. Specifically, arrays of doped graphene nanodisks display full absorption when supported on a substrate under total internal reflection and also when lying on a dielectric layer coating a metal. Our results are relevant for infrared light detectors and sources, which can be made tunable via electrostatic doping of graphene. © 2012 American Physical Society.

Santiveri C.M.,CSIC - Institute of Physical Chemistry "Rocasolano"
Biopolymers | Year: 2010

Tryptophan plays important roles in protein stability and recognition despite its scarcity in proteins. Except as fluorescent groups, they have been used rarely in peptide design. Nevertheless, Trp residues were crucial for the stability of some designed minimal proteins. In 2000, Trp-Trp pairs were shown to contribute more than any other hydrophobic interaction to the stability of β-hairpin peptides. Since then, Trp-Trp pairs have emerged as a paradigm for the design of stable β-hairpins, such as the Trpzip peptides. Here, we analyze the nature of the stabilizing capacity of Trp-Trp pairs by reviewing the β-hairpin peptides containing Trp-Trp pairs described up to now, the spectroscopic features and geometry of the Trp-Trp pairs, and their use as binding sites in β-hairpin peptides. To complete the overview, we briefly go through the other relevant β-hairpin stabilizing Trp-non-Trp interactions and illustrate the use of Trp in the design of short peptides adopting α-helical and mixed α/β motifs. This review is of interest in the field of rational design of proteins, peptides, peptidomimetics, and biomaterials. 2010 Wiley Periodicals, Inc.

Almarza N.G.,CSIC - Institute of Physical Chemistry "Rocasolano"
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | Year: 2012

We report Monte Carlo simulations that show a closed-loop liquid-vapor equilibrium in a pure substance. This finding has been achieved on a two-dimensional lattice model for patchy particles that can form network fluids. We have considered related models with a slightly different patch distribution in order to understand the features of the distribution of patches on the surface of the particles that make possible the presence of the closed-loop liquid-vapor equilibrium, and its relation to the phase diagram containing so-called empty liquids. Finally we discuss the likelihood of finding the closed-loop liquid-vapor equilibria on related models for three-dimensional models of patchy particles in the continuum, and speculate on the possible relationship between the mechanism behind the closed-loop liquid-vapor equilibrium of our simple lattice model and the salt-induced reentrant condensation found in complex systems. © 2012 American Physical Society.

Hermoso J.A.,CSIC - Institute of Physical Chemistry "Rocasolano"
Structure | Year: 2014

CAD is a large multifunctional polypeptide that initiates and controls the de novo biosynthesis of pyrimidines in animals. In this issue of Structure, Grande-García and colleagues provide the first atomic information of this antitumoral target by reporting the crystal structure of the dihydroorotase domain of human CAD. © 2014 Elsevier Ltd.

Thongrattanasiri S.,CSIC - Institute of Physical Chemistry "Rocasolano" | Manjavacas A.,CSIC - Institute of Physical Chemistry "Rocasolano" | Garcia De Abajo F.J.,CSIC - Institute of Physical Chemistry "Rocasolano" | Garcia De Abajo F.J.,University of Southampton
ACS Nano | Year: 2012

Graphene plasmons are emerging as an alternative solution to noble metal plasmons, adding the advantages of tunability via electrostatic doping and long lifetimes. These excitations have been so far described using classical electrodynamics, with the carbon layer represented by a local conductivity. However, the question remains, how accurately is such a classical description representing graphene? What is the minimum size for which nonlocal and quantum finite-size effects can be ignored in the plasmons of small graphene structures? Here, we provide a clear answer to these questions by performing first-principles calculations of the optical response of doped nanostructured graphene obtained from a tight-binding model for the electronic structure and the random-phase approximation for the dielectric response. The resulting plasmon energies are in good agreement with classical local electromagnetic theory down to ∼10 nm sizes, below which plasmons split into several resonances that emphasize the molecular character of the carbon structures and the quantum nature of their optical excitations. Additionally, finite-size effects produce substantial plasmon broadening compared to homogeneous graphene up to sizes well above 20 nm in nanodisks and 10 nm in nanoribbons. The atomic structure of edge terminations is shown to be critical, with zigzag edges contributing to plasmon broadening significantly more than armchair edges. This study demonstrates the ability of graphene nanostructures to host well-defined plasmons down to sizes below 10 nm, and it delineates a roadmap for understanding their main characteristics, including the role of finite size and nonlocality, thus providing a solid background for the emerging field of graphene nanoplasmonics. © 2012 American Chemical Society.

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