Angel Rubio

A Dynamic Landscape from Femtoseconds to Minutes for Excess Electrons at Ice-Metal Interfaces (2009)

Bovensiepen, Uwe, Gahl, Cornelius, Stähler, Julia, Bockstedte, Michel, Meyer, Michael, Baletto, Francesca, ...

Stabilization of excess electrons is studied at crystalline ice-metal interfaces by femtosecond time-resolved two-photon photoelectron spectroscopy and ab initio calculations. Following optical...

3 Electronic Structure Calculations for Nanomolecular Systems (2008)

Rosa Di Felice, Arrigo Calzolari, Daniele Varsano, Angel Rubio, Centro Mixto Csic

Abstract. The electronic structure constitutes the fundamentals on which a reliable quantitative knowledge of the electrical properties of materials should be based. Here, we first present an...

A modified Ehrenfest formalism for efficient large-scale ab initio molecular dynamics (2008)

Andrade, Xavier, Castro, Alberto, Zueco, David, Alonso, J. L., Echenique, Pablo, Falceto, Fernando, ...

We present in detail the recently derived ab-initio molecular dynamics (AIMD) formalism [Phys. Rev. Lett. 101 096403 (2008)], which due to its numerical properties, is ideal for simulating the...

Renormalization of Molecular Quasiparticle Levels at Metal-Molecule Interfaces: Trends Across Binding Regimes (2008)

Thygesen, Kristian S., Rubio, Angel

When an electron or a hole is added into an orbital of an adsorbed molecule the substrate electrons will rearrange in order to screen the added charge. This results in a reduction of the electron...

Cluster-surface and cluster-cluster interactions: Ab initio calculations and modeling of van der Waals forces (2008)

Botti, Silvana, Castro, Alberto, Andrade, Xavier, Rubio, Angel, Marques, Miguel A. L.

We present fully ab-initio calculations of van der Waals coefficients for two different situations: i) the interaction between hydrogenated silicon clusters; and ii) the interactions between these...

Site-selective conductance of sidewall functionalized carbon nanotubes (2008)

Garcia-Lastra, Juan Maria, Thygesen, Kristian S., Strange, Mikkel, Rubio, Angel

We use DFT to study the effect of molecular adsorbates on the conductance of metallic carbon nanotubes. The five molecules considered (NO2, NH2, H, COOH, OH) lead to similar scattering of the...

SPACE: an algorithm to predict and quantify alternatively spliced isoforms using microarrays (2008)

Anton, Miguel A, Gorostiaga, Dorleta, Guruceaga, Elizabeth, Segura, Victor, Carmona-Saez, Pedro, Pascual-Montano, Alberto, ...

Abstract Exon and exon+junction microarrays are promising tools for studying alternative splicing. Current analytical tools applied to these arrays lack two relevant features: the ability to predict...

SPACE: an algorithm to predict and quantify alternatively spliced isoforms using microarrays (2008)

Antón, Miguel A., Gorostiaga, Dorleta, Guruceaga, Elizabeth, Segura, Víctor, Carmona-Sáez, Pedro, Pascual-Montano, Alberto, ...

20 pages, 13 figures.-- Supplementary material available at: http://genomebiology.com/2008/9/2/R46/additional/ (Additional data file 1: 22 Figures. Additional data file 2: Matlab data files).--...

Ab initio study of transport properties in defected carbon nanotubes: an O(N) approach (2008)

Biel, Blanca, Garcia-Vidal, F. J., Rubio, Angel, Flores, Fernando

A combination of ab initio simulations and linear-scaling Green's functions techniques is used to analyze the transport properties of long (up to one micron) carbon nanotubes with realistic disorder....

Ultrafast Electron-Phonon Decoupling in Graphite (2007)

Ishioka, Kunie, Hase, Muneaki, Kitajima, Masahiro, Wirtz, Ludger, Rubio, Angel, Petek, Hrvoje

We report the ultrafast dynamics of the 47.4 THz coherent phonons of graphite interacting with a photoinduced non-equilibrium electron-hole plasma. Unlike conventional materials, upon photoexcitation...

Efficient formalism for large scale ab initio molecular dynamics based on time-dependent density functional theory (2007)

Alonso, J. L., Andrade, Xavier, Echenique, Pablo, Falceto, Fernando, Prada-Gracia, Diego, Rubio, Angel

A new "on the fly" method to perform Born-Oppenheimer ab initio molecular dynamics (AIMD) is presented. Inspired by Ehrenfest dynamics in time-dependent density functional theory, the electronic...

On the use of Neumann's principle for the calculation of the polarizability tensor of nanostructures (2007)

Oliveira, Micael J. T., Castro, Alberto, Marques, Miguel A. L., Rubio, Angel

The polarizability measures how the system responds to an applied electrical field. Computationally, there are many different ways to evaluate this tensorial quantity, some of which rely on the...

Optical saturation driven by exciton confinement in molecular-chains: a TDDFT study (2007)

Varsano, Daniele, Marini, Andrea, Rubio, Angel

We have identified excitonic confinement in one-dimensional molecular chains (i.e. polyacetylene and H$_2$) as the main driving force for the saturation of the chain polarizability as a function of...

Conserving GW scheme for nonequilibrium quantum transport in molecular contacts (2007)

Thygesen, Kristian S., Rubio, Angel

We give a detailed presentation of our recent scheme to include correlation effects in molecular transport calculations using the GW approximation within the non-equilibrium Keldysh formalism. We...

Raman spectra of BN-nanotubes: Ab-initio and bond-polarizability model calculations (2007)

Wirtz, Ludger, Lazzeri, Michele, Mauri, Francesco, Rubio, Angel

We present it ab-initio calculations of the non-resonant Raman spectra of zigzag and armchair BN nanotubes. In comparison, we implement a generalized bond-polarizability model where the parameters...

A time-dependent density functional theory scheme for efficient calculations of dynamic (hyper)polarizabilities (2007)

Andrade, Xavier, Botti, Silvana, Marques, Miguel A. L., Rubio, Angel

We present an efficient perturbative method to obtain both static and dynamic polarizabilities and hyperpolarizabilities of complex electronic systems. This approach is based on the solution of a...

Electronic conduction in multi-walled carbon nanotubes: Role of intershell coupling and incommensurability (2007)

Roche, Stephan, Triozon, François, Rubio, Angel, Mayou, Didier

Geometry incommensurability between weakly coupled shells in multi-walled carbon nanotubes is shown to be the origin of unconventional electronic conduction mechanism, power-law scaling of the...

Backscattering in carbon nanotubes : role of quantum interference effects (2007)

Roche, Stephan, Triozon, Francois, Rubio, Angel

For similar disorder, the backscattering contribution to the conductivity, irrelevant for metallic single-walled carbon nanotubes, is proved to become more significant for doped semiconducting...

Conduction mechanism and magnetotransport in multi-walled carbon nanotubes (2007)

Roche, Stephan, Triozon, Francois, Rubio, Angel, Mayou, D.

We report on a numerical study of quantum diffusion over micron lengths in defect-free multi-walled nanotubes. The intershell coupling allows the electron spreading over several shells, and when...

Excitonic effects in solids described by time-dependent density functional theory (2007)

Reining, Lucia, Olevano, Valerio, Rubio, Angel, Onida, Giovanni

Starting from the many-body Bethe-Salpeter equation we derive an exchange-correlation kernel $f_{xc}$ that reproduces excitonic effects in bulk materials within time-dependent density functional...

Non-equilibrium GW approach to quantum transport in nano-scale contacts (2006)

Thygesen, Kristian S., Rubio, Angel

Correlation effects within the GW approximation have been incorporated into the Keldysh non-equilibrium transport formalism. We show that GW describes the Kondo effect and the zero-temperature...

Ab initio simulations of excited carrier dynamics in carbon nanotubes (2006)

Miyamoto, Yoshiyuki, Rubio, Angel, Tomanek, David

Combining time-dependent density functional calculations for electrons with molecular dynamics simulations for ions, we investigate the dynamics of excited carriers in a (3,3) carbon nanotube at...

Time dependent transport phenomena (2006)

Stefanucci, Gianluca, Kurth, Stefan, Gross, E. K. U., Rubio, Angel

The aim of this review is to give a pedagogical introduction to our recently proposed ab initio theory of quantum transport.

An exact Coulomb cutoff technique for supercell calculations (2006)

Rozzi, Carlo A., Varsano, Daniele, Marini, Andrea, Gross, Eberhard K. U., Rubio, Angel

We present a new reciprocal space analytical method to cutoff the long range interactions in supercell calculations for systems that are infinite and periodic in 1 or 2 dimensions, extending previous...

The Enhancement of Metallic Silver Monomer Evaporation by the Adhesion of Polar Molecules to Silver Nanocluster Ions (2006)

Fagerquist, Clifton, Sensharma, Dilip K., Rubio, Angel, Cohen, Marvin L., El-Sayed, M. A.

We have compared the metallic evaporation channels from metastable Ag(X=5,7,11)(AgI)(Y=1-4)(+) clusters in the 1st FFR of a double focussing mass spectrometer with that of the corresponding pure...

Anderson localization in carbon nanotubes: defect density and temperature effects (2005)

Biel, Blanca, Garcia-Vidal, F. J., Rubio, Angel, Flores, Fernando

The role of irradiation induced defects and temperature in the conducting properties of single-walled (10,10) carbon nanotubes has been analyzed by means of a first-principles approach. We find that...

First-Principle Description of Correlation Effects in Layered Materials (2005)

Marini, Andrea, García-González, P., Rubio, Angel

We present a first-principles description of anisotropic materials characterized by having both weak (dispersion-like) and strong covalent bonds, based on the Adiabatic--Connection...

Excitons in boron nitride nanotubes: dimensionality effects (2005)

Wirtz, Ludger, Marini, Andrea, Rubio, Angel

We show that the optical absorption spectra of boron nitride (BN) nanotubes are dominated by strongly bound excitons. Our first-principles calculations indicate that the binding energy for the first...

Excitonic effects in optical absorption and electron-energy loss spectra of hexagonal boron nitride (2005)

Wirtz, Ludger, Marini, Andrea, Gruning, Myrta, Rubio, Angel

A new interpretation of the optical and energy-loss spectra of hexagonal boron nitride is provided based on first-principle calculations. We show that both spectra cannot be explained by...

Asymptotics of the dispersion interaction: analytic benchmarks for van der Waals energy functionals (2005)

Dobson, John F., White, Angela, Rubio, Angel

We show that the usual sum of $R^{-6}$ contributions from elements separated by distance $R$ can give \emph{qualitatively} wrong results for the electromagnetically non-retarded van der Waals...

Raman spectra of BN-nanotubes: Ab-initio and bond-polarizability model calculations (2005)

Wirtz, Ludger, Lazzeri, Michele, Mauri, Francesco, Rubio, Angel

We present it ab-initio calculations of the non-resonant Raman spectra of zigzag and armchair BN nanotubes. In comparison, we implement a generalized bond-polarizability model where the parameters...

Nonuniversality of the dispersion interaction: analytic benchmarks for van der Waals energy functionals (2005)

Dobson, John F., Rubio, Angel

We highlight the non-universality of the asymptotic behavior of dispersion forces, such that a sum of inverse sixth power contributions is often inadequate. We analytically evaluate the...

Raman spectra of BN-nanotubes: Ab-initio and bond-polarizability model calculations (2005)

Wirtz, Ludger, Lazzeri, Michele, Mauri, Francesco, Rubio, Angel

We present it ab-initio calculations of the non-resonant Raman spectra of zigzag and armchair BN nanotubes. In comparison, we implement a generalized bond-polarizability model where the parameters...

Raman spectra of BN-nanotubes: Ab-initio and bond-polarizability model calculations (2005)

Wirtz, Ludger, Lazzeri, Michele, Mauri, Francesco, Rubio, Angel

We present it ab-initio calculations of the non-resonant Raman spectra of zigzag and armchair BN nanotubes. In comparison, we implement a generalized bond-polarizability model where the parameters...

The phonon dispersion of graphite revisited (2004)

Wirtz, Ludger, Rubio, Angel

We review calculations and measurements of the phonon-dispersion relation of graphite. First-principles calculations using density-functional theory are generally in good agreement with the...

Band structure of boron doped carbon nanotubes (2003)

Wirtz, Ludger, Rubio, Angel

We present {\it ab initio} and self-consistent tight-binding calculations on the band structure of single wall semiconducting carbon nanotubes with high degrees (up to 25 %) of boron substitution....

Optical absorption and electron energy loss spectra of carbon and boron nitride nanotubes: a first principles approach (2003)

Marinopoulos, A. G., Wirtz, Ludger, Marini, Andrea, Olevano, Valerio, Rubio, Angel, Reining, Lucia

We present results for the optical absorption spectra of small-diameter single-wall carbon and boron nitride nanotubes obtained by {\it ab initio} calculations in the framework of time-dependent...

Time and energy-resolved two photon-photoemission of the Cu(100) and Cu(111) metal surfaces (2003)

Varsano, Daniele, Marques, M. A. L., Rubio, Angel

We present calculations on energy- and time-resolved two-photon photoemission spectra of images states in Cu(100) and Cu(111) surfaces. The surface is modeled by a 1D effective potential and the...

GARBAN: genomic analysis and rapid biological annotation of cDNA microarray and proteomic data (2003)

Martínez-Cruz, Luis A., Rubio, Angel, Martínez-Chantar, María L., Labarga, Alberto, Barrio, Isabel, Podhorski, Adam, ...

Summary: Genomic Analysis and Rapid Biological ANnotation (GARBAN) is a new tool that provides an integrated framework to analyze simultaneously and compare multiple data sets derived from microarray...

Quasiparticle bandstructure effects on the {\it d} hole lifetimes of copper within the GW approximation (2002)

Marini, Andrea, Del Sole, Rodolfo, Rubio, Angel, Onida, Giovanni

We investigate the lifetime of {\it d} holes in copper within a {\it first--principle} $GW$ approximation. At the $G_0W_0$ level the lifetime of the topmost {\it d} bands are in agreement with the...

Excited states dynamics in time-dependent density functional theory: high-field molecular dissociation and harmonic generation (2002)

Castro, Alberto, Marques, M. A. L., Alonso, Julio A., Bertsch, George F., Rubio, Angel

We present a theoretical description of femtosecond laser induced dynamics of the hydrogen molecule and of singly ionised sodium dimers, based on a real-space, real-time, implementation of...

Can optical spectroscopy directly elucidate the ground state of C20? (2001)

Castro, Alberto, Marques, M. A. L., Alonso, Julio A., Bertsch, George F., Yabana, K., Rubio, Angel

The optical response of the lowest energy members of the C20 family is calculated using time-dependent density functional theory within a real-space, real-time scheme. Significant differences are...

Excitonic effects in solids described by time-dependent density functional theory (2001)

Reining, Lucia, Olevano, Valerio, Rubio, Angel, Onida, Giovanni

Starting from the many-body Bethe-Salpeter equation we derive an exchange-correlation kernel $f_{xc}$ that reproduces excitonic effects in bulk materials within time-dependent density functional...

Stochastic Heterostructures in B/N-Doped Carbon Nanotubes (2001)

Lammert, Paul E., Crespi, Vincent H., Rubio, Angel

Carbon nanotubes are one-dimensional and very narrow. These obvious facts imply that under doping with boron and nitrogen, microscopic doping inhomogeneity is much more important than for bulk...

Electronic conduction in multi-walled carbon nanotubes: Role of intershell coupling and incommensurability (2001)

Roche, Stephan, Triozon, François, Rubio, Angel, Mayou, Didier

Geometry incommensurability between weakly coupled shells in multi-walled carbon nanotubes is shown to be the origin of unconventional electronic conduction mechanism, power-law scaling of the...

Anomalous Quasiparticle Lifetime in Graphite: Band Structure Effects (2001)

Spataru, Catalin D., Cazalilla, Miguel A., Rubio, Angel, Benedict, Lorin X., Echenique, Pedro M., Louie, Steven G.

We report ab initio calculation of quasiparticle lifetimes in graphite, as determined from the imaginary part of the self-energy operator within the GW aproximation. The inverse lifetime in the...

Backscattering in carbon nanotubes : role of quantum interference effects (2001)

Roche, Stephan, Triozon, Francois, Rubio, Angel

For similar disorder, the backscattering contribution to the conductivity, irrelevant for metallic single-walled carbon nanotubes, is proved to become more significant for doped semiconducting...

Conduction mechanism and magnetotransport in multi-walled carbon nanotubes (2001)

Roche, Stephan, Triozon, Francois, Rubio, Angel, Mayou, D.

We report on a numerical study of quantum diffusion over micron lengths in defect-free multi-walled nanotubes. The intershell coupling allows the electron spreading over several shells, and when...

Assessment of exchange-correlation functionals for the calculation of dynamical properties of small clusters in TDDFT (2001)

Marques, M. A. L., Castro, Alberto, Rubio, Angel

We present a detailed study of different exchange-correlation (xc) functionals in describing the dynamical properties of finite systems. For that purpose, we calculated the static polarizabilities,...

Solution of Poisson's equation for finite systems using plane wave methods (2000)

Castro, Alberto, Rubio, Angel, Stott, M. J.

Reciprocal space methods for solving Poisson's equation for finite charge distributions are investigated. Improvements to previous proposals are presented, and their performance is compared in the...

A real-space, rela-time method for the dielectric function (2000)

Bertsch, G. F., Rubio, Angel, Yabana, K.

We present an algorithm to calculate the linear response of periodic systems in the time-dependent density functional thoery, using a real-space representation of the electron wave functions and...

Comparision of direct and Fourier space techniques in time-dependent density functional theory (2000)

Bertsch, G. F., Rubio, Angel, Yabana, K.

Several techniques have appeared in the literatuare to solve the equations of time-dependent density functional theory. We compare the efficiency of different methods based on mesh representations of...

A Mechanism for Cutting Carbon Nanotubes with a Scanning Tunneling Microscope (2000)

Rubio, Angel, Apell, S. Peter, Venema, Liesbeth C., Dekker, Cees

We discuss the local cutting of single-walled carbon nanotubes by a voltage pulse to the tip of a scanning tunneling microscope. The tip voltage ($\mid V \mid \ge $~3.8 eV) is the key physical...

Spectroscopic Properties and STM Images of Carbon Nanotubes (1999)

Rubio, Angel

We present a theoretical study of the role of the local environment in the electronic properties of carbon nanotubes: isolated single- and multi-wall nanotubes, nanotube-ropes, tubes supported on...

Theoretical Study of One-dimensional Chains of Metal Atoms in Nanotubes (1995)

Rubio, Angel, Miyamoto, Yoshiyuki, Blase, X., Cohen, Marvin L., Louie, Steven G.

Using first-principles total-energy pseudopotential calculations, we have studied the properties of chains of potassium and aluminum in nanotubes. For BN tubes, there is little interaction between...

Density-Functional Theory of the nonlinear optical susceptibility: application to cubic semiconductors (1995)

Corso, Andrea Dal, Mauri, Francesco, Rubio, Angel

We present a general scheme for the computation of the time dependent (TD) quadratic susceptibility ($\chi^{(2)}$) of an extended insulator obtained by applying the `$2n+1$' theorem to the action...

Functional proteomics of nonalcoholic steatohepatitis: Mitochondrial proteins as targets of S-adenosylmethionine

Santamaría, Enrique, Avila, Matías A., Latasa, M. Ujue, Rubio, Angel, Martín-Duce, Antonio, Lu, Shelly C., ...

Recent work shows that S-adenosylmethionine (AdoMet) helps maintain normal liver function as chronic hepatic deficiency results in spontaneous development of steatohepatitis and hepatocellular...

Functional proteomics of nonalcoholic steatohepatitis: Mitochondrial proteins as targets of S-adenosylmethionine

Santamaría, Enrique, Avila, Matías A., Latasa, M. Ujue, Rubio, Angel, Martín-Duce, Antonio, Lu, Shelly C., ...

Recent work shows that S-adenosylmethionine (AdoMet) helps maintain normal liver function as chronic hepatic deficiency results in spontaneous development of steatohepatitis and hepatocellular...

SPACE: an algorithm to predict and quantify alternatively spliced isoforms using microarrays

Anton, Miguel A, Gorostiaga, Dorleta, Guruceaga, Elizabeth, Segura, Victor, Carmona-Saez, Pedro, Pascual-Montano, Alberto, ...

SPACE is an algorithm developed to predict and quantify the pre-mRNA splicing structure of transcripts using exon and ‘exon plus junction’ microarray data.