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Angel Rubio

Publications and source records attributed to Angel Rubio.

At least 19 recordsLinked to original sources
PubMed2006

Real-time ab initio simulations of excited carrier dynamics in carbon nanotubes.

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 different temperatures. Following an hnu=6.8 eV photoexcitation, the carrier decay is initially dominated by efficient coupling to electronic degrees of freedom. At room temperature, the excitation gap is reduced to nearly half its initial value after approximately 230 fs, where coupling to ionic motion starts dominating the decay. We show that the onset point and damping rate in the phonon regime change with initial ion velocities, a manifestation of temperature-dependent coupling between electronic and ionic degrees of freedom.

Journal Article↗
PubMed2006

Scanning tunneling spectroscopy simulations of poly(3-dodecylthiophene) chains adsorbed on highly oriented pyrolytic graphite.

We report on a hybrid scheme to perform efficient and accurate simulations of scanning tunneling spectroscopy (STS) of molecules weakly bonded to surfaces. Calculations are based on a tight binding (TB) technique, including a self-consistent calculation of the electronic structure of the molecule, to predict STS conductance spectra. The use of a local basis makes our model easily applicable to systems with several hundreds of atoms. We performed first-principles density-functional calculations to extract the geometrical and electronic properties of the system. In this way, we can include, in the TB scheme, the effects of structural relaxation upon adsorption on the electronic structure of the molecule. This approach is applied to the study of regioregular poly(3-dodecylthiophene) polymer chains adsorbed on highly oriented pyrolytic graphite. Results of spectroscopic calculations are discussed and compared with recently obtained experimental data.

Journal Article↗
PubMed2006

Density functionals from many-body perturbation theory: the band gap for semiconductors and insulators.

Theoretically the Kohn-Sham band gap differs from the exact quasiparticle energy gap by the derivative discontinuity of the exchange-correlation functional. In practice for semiconductors and insulators the band gap calculated within any local or semilocal density approximations underestimates severely the experimental energy gap. On the other hand, calculations with an "exact" exchange potential derived from many-body perturbation theory via the optimized effective potential suggest that improving the exchange-correlation potential approximation can yield a reasonable agreement between the Kohn-Sham band gap and the experimental gap. The results in this work show that this is not the case. In fact, we add to the exact exchange the correlation that corresponds to the dynamical (random phase approximation) screening in the GW approximation. This accurate exchange-correlation potential provides band structures similar to the local density approximation with the corresponding derivative discontinuity that contributes 30%-50% to the energy gap. Our self-consistent results confirm substantially the results for Si and other semiconductors obtained perturbatively [R. W. Godby et al., Phys. Rev. B 36, 6497 (1987)] and extend the conclusion to LiF and Ar, a wide-gap insulator and a noble-gas solid.

Journal Article↗
PubMed2006

A TDDFT study of the excited states of DNA bases and their assemblies.

We present a detailed study of the optical absorption spectra of DNA bases and base pairs, carried out by means of time dependent density functional theory. The spectra for the isolated bases are compared to available theoretical and experimental data and used to assess the accuracy of the method and the quality of the exchange-correlation functional. Our approach turns out to be a reliable tool to describe the response of the nucleobases. Furthermore, we analyze in detail the impact of hydrogen bonding and pi-stacking in the calculated spectra for both Watson-Crick base pairs and Watson-Crick stacked assemblies. We show that the reduction of the UV absorption intensity (hypochromicity) for light polarized along the base-pair plane depends strongly on the type of interaction. For light polarized perpendicular to the basal plane, the hypochromicity effect is reduced, but another characteristic is found, namely a blue shift of the optical spectrum of the base-assembly compared to that of the isolated bases. The use of optical tools as fingerprints for the characterization of the structure (and type of interaction) is extensively discussed.

Base Pairing↗
PubMed2006

Electronic structure and excitations in oligoacenes from ab initio calculations.

Oligoacenes C(4n+2)H(2n+4) (n=2,...,6) are studied using a variety of ab initio methods. Density functional theory (DFT) optimized geometries were in good agreement with experiment. Vertical and adiabatic ionization potentials and electron affinities were computed with DFT and it was found that standard exchange-correlation (xc) functionals underestimate ionization potentials in oligoacenes. Possible reasons for this underestimation are discussed. Low lying electronic excitations were computed using time-dependent density functional theory, configuration interaction singles, and configuration interaction singles with approximate treatment of doubles. In agreement with earlier work, time-dependent DFT in conjunction with standard xc-energy functionals substantially underestimates the lowest (p) singlet-singlet electronic transition.

Journal Article↗
PubMed2006

First-principles description of correlation effects in layered materials.

We present a first-principles description of anisotropic materials characterized by having both weak (dispersionlike) and strong covalent bonds, based on the adiabatic-connection fluctuation-dissipation theorem with density functional theory. For hexagonal boron nitride the in-plane and out-of-plane bonding as well as vibrational dynamics are well described both at equilibrium and when the layers are pulled apart. Bonding in covalent and ionic solids is also described. The formalism allows us to ping down the deficiencies of common exchange-correlation functionals and provides insight toward the inclusion of dispersion interactions into the correlation functional.

Journal Article↗
PubMed2006

Excitons in boron nitride nanotubes: dimensionality effects.

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 and dominant excitonic peak depends sensitively on the dimensionality of the system, varying from 0.7 eV in bulk hexagonal BN via 2.1 eV in the single sheet of BN to more than 3 eV in the hypothetical (2, 2) tube. The strongly localized nature of this exciton dictates the fast convergence of its binding energy with increasing tube diameter towards the sheet value. The absolute position of the first excitonic peak is almost independent of the tube radius and system dimensionality. This provides an explanation for the observed "optical gap" constancy for different tubes and bulk hexagonal BN.

Journal Article↗
PubMed2006

Asymptotics of the dispersion interaction: analytic benchmarks for van der Waals energy functionals.

We show that the usual sum of R-6 contributions from elements separated by distance R can give qualitatively wrong results for the electromagnetically nonretarded van der Waals interaction between nonoverlapping bodies. This occurs for anisotropic nanostructures that have a zero electronic energy gap, such as metallic nanotubes or nanowires, and nanolayered systems including metals and graphene planes. In all these cases our analytic microscopic calculations give an interaction falling off with a power of separation different from the conventional value. We discuss implications for van der Waals energy functionals. The new nanotube interaction might be directly observable at submicron separations.

Journal Article↗
PubMed2006

GARBAN II: an integrative framework for extracting biological information from proteomic and genomic data.

Genomic and proteomic analyses generate a massive amount of data that requires specific bioinformatic tools for its management and interpretation. GARBAN II, developed from the previous GARBAN platform, provides an integrated framework to simultaneously analyse and compare multiple datasets from DNA microarrays and proteomic studies. The general architecture, gene classification and comparison, and graphical representation have been redesigned to ensure a user-friendly feature and to improve the capabilities and efficiency of this system. Additionally, GARBAN II has been extended with new applications to display networks of coexpressed genes and to integrate access to BioRag and MotifScanner so as to facilitate the holistic analysis of users' data.

Animals↗
PubMed2006

Probing the electronic properties of self-organized poly(3-dodecylthiophene) monolayers by two-dimensional scanning tunneling spectroscopy imaging at the single chain scale.

Regioregular poly(3-dodecylthiophene) films self-organized on highly oriented pyrolytic graphite have been investigated by scanning tunneling microscopy and two-dimensional scanning tunneling spectroscopy (STS). Simulated spectra in very good agreement with the experimental data have been obtained by a method combining ab initio and semiempirical approaches, which allows a careful discussion of the polymer electronic states. From the experimental data, with the support of modeling, it is shown that the STS spectra give a direct access to the polymer semiconducting band gap without noticeable charge-transfer effects from the substrate. Spectroscopic images are achieved at the single chain scale, which allows scrutinizing the electronic consequences of chain folds and pi-stacking effects through spectroscopic contrasts. While chain folds do not locally increase the polymer band gap more than a few tens of millielectonvolt, a striking widening of the STS conductance gap is observed in the case of electronic tunneling through two interacting polymer layers. Scenarios based on nonplanar configuration of thiophene cycles within the second layer or variations of the charge screening effects are proposed to explain this phenomenon.

Computer Simulation↗
PubMed2005

Anderson localization in carbon nanotubes: defect density and temperature effects.

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 divacancies modify strongly the energy dependence of the differential conductance, reducing also the number of contributing channels from two (ideal) to one. A small number of divacancies (5-9) brings up strong Anderson localization effects and a seemly universal curve for the resistance as a function of the number of defects. It is also shown that low temperatures, about 15-65 K, are enough to smooth out the fluctuations of the conductance without destroying the exponential dependence of the resistivity as a function of the tube length.

Journal Article↗
PubMed2005

Differential virial theorem in relation to a sum rule for the exchange-correlation force in density-functional theory.

Holas and March [Phys. Rev. A. 51, 2040 (1995)] gave a formally exact theory for the exchange-correlation (xc) force F(xc)(r)= -inverted Deltaupsilon(xc)(r) associated with the xc potential upsilon(xc)(r) of the density-functional theory in terms of low-order density matrices. This is shown in the present study to lead, rather directly, to the determination of a sum rule nF(xc)=0 relating the xc force with the ground-state density n(r). Some connection is also made with an earlier result relating to the external potential by Levy and Perdew [Phys. Rev. A. 32, 2010 (1985)] and with the quite recent study of Joubert [J. Chem. Phys. 119, 1916 (2003)] relating to the separation of the exchange and correlation contributions.

Absorption↗
PubMed2005

Optical absorption of the blue fluorescent protein: a first-principles study.

An extensive study of the optical absorption spectra of the blue fluorescent protein (BFP) is presented. We investigate different protonation states of the chromophore (neutral, anionic, and cationic) and analyze the role of the protein environment and of thermal fluctuations. The role of the environment is 2-fold: (i) it induces structural modifications of the gas-phase chromophore, the most important being the torsion of the imida rings; and (ii) it makes a local-field modification of the external electromagnetic field. It turns out that the torsion of the imida rings shifts significantly the gas-phase spectra to lower energies, whereas the consistent inclusion of the closest residues field produces only minor modifications on the spectra. From all of the configurations studied, the neutral cis-HSD and the anionic HSA seem to be the most likely candidates to explain the experimental spectrum. Furthermore, the present results clearly rule out the presence of the cationic protonation state (HSP) of the chromophore. However, a better description of the measured experimental absorption data may be obtained when the temperature fluctuations of the floppy torsional motion of the two imida rings are included. Our results, together with previous work on the green fluorescent protein, demonstrate the power of combining time-dependent density functional calculations and optical absorption measurements to discern the relevant chemical information on the nature and state of chromopeptides.

Cations↗
PubMed2005

An in-depth and updated perspective on determinants of cervical cancer screening among central Appalachian women.

Although cervical cancer rates in the U.S. have declined sharply, certain groups remain at elevated risk, including Appalachian women. To establish culturally-relevant cervical cancer prevention programs requires a comprehensive, current understanding of the factors which influence women's decisions to undergo Pap tests. Since most studies that found low rates of Pap test use in Appalachia were carried out decades ago, an in-depth update is warranted. Local, trained interviewers conducted interviews with rarely or never screened Appalachian women from Kentucky and West Virginia. Sessions were tape recorded, transcribed, and content analyzed. Participants (N = 25) suggested the following positive influences on obtaining screening: having an orientation toward the use of preventive health services; having health insurance and access to a good medical environment; and maintaining a flexible enough schedule to keep appointments. Screening barriers included: fear of subjecting oneself to medical scrutiny because of obesity or being a smoker; inadequate health care access such as clinician shortages, scarcity of specialty providers, long travel time to services, and clinic schedules that do not accommodate working women; and lack of providers' recommendations. Rarely mentioned were some previously reported factors including male relatives' refusal to permit Pap tests, concern over privacy, and lack of belief in Pap tests.

Adult↗
PubMed2004

Propagators for the time-dependent Kohn-Sham equations.

In this paper we address the problem of the numerical integration of the time-dependent Schrodinger equation i partial differential (t)phi=Hphi. In particular, we are concerned with the important case where H is the self-consistent Kohn-Sham Hamiltonian that stems from time-dependent functional theory. As the Kohn-Sham potential depends parametrically on the time-dependent density, H is in general time dependent, even in the absence of an external time-dependent field. The present analysis also holds for the description of the excited state dynamics of a many-electron system under the influence of arbitrary external time-dependent electromagnetic fields. Our discussion is separated in two parts: (i) First, we look at several algorithms to approximate exp(A), where A is a time-independent operator [e.g., A=-iDeltatH(tau) for some given time tau]. In particular, polynomial expansions, projection in Krylov subspaces, and split-operator methods are investigated. (ii) We then discuss different approximations for the time-evolution operator, such as the midpoint and implicit rules, and Magnus expansions. Split-operator techniques can also be modified to approximate the full time-dependent propagator. As the Hamiltonian is time dependent, problem (ii) is not equivalent to (i). All these techniques have been implemented and tested in our computer code OCTOPUS, but can be of general use in other frameworks and implementations.

Journal Article↗
PubMed2004

The Appalachia Cancer Network: cancer control research among a rural, medically underserved population.

Residents of Appalachia, especially those in rural Appalachia, are generally considered to be medically underserved. In fact, cancer mortality in Appalachia, especially in rural Appalachia, is higher than it is in the remainder of the United States. Developing from the Appalachia Leadership Initiative on Cancer, the Appalachia Cancer Network (ACN) is a network of academic and community organizations that seek to conduct surveillance, intervention, and dissemination research to reduce this excess cancer burden in Appalachia. The purpose of this report is to (1) describe the approach to cancer control research in ACN, a Special Population Network, among the medically underserved of Appalachia, and (2) to put forward observations from this experience to enhance the research of other academic and community networks among underserved populations. ACN has instituted a conceptual model, organizational structure, and other methods to foster this research and to develop junior and community-based investigators. Important issues and questions related to the effectiveness of such research networks have also been articulated.

Appalachian Region↗