Towards First-principles Electrochemistry

Chemisorbed molecules at a fuel cell electrode are a very sensitive probe of the surrounding electrochemical environment, and one that can be accurately monitored with different spectroscopic techniques. We develop a comprehensive electrochemical model to study molecular chemisorption at either constant charge or fixed applied voltage, and calculate from first principles the voltage dependence of vibrational frequencies -- the vibrational Stark effect -- for CO adsorbed on close-packed platinum electrodes. The predicted vibrational Stark slopes are found to be in very good agreement with experimental electrochemical spectroscopy data, thereby resolving previous controversies in the quantitative interpretation of in-situ experiments and elucidating the relation between canonical and grand-canonicaldescriptions of vibrational surface phenomena.Comment: 10 pages, 2 figure

Protein Repeats from First Principles

Some natural proteins display recurrent structural patterns. Despite being highly similar at the tertiary structure level, repeating patterns within a single repeat protein can be extremely variable at the sequence level. We use a mathematical definition of a repetition and investigate the occurrences of these in sequences of different protein families. We found that long stretches of perfect repetitions are infrequent in individual natural proteins, even for those which are known to fold into structures of recurrent structural motifs. We found that natural repeat proteins are indeed repetitive in their families, exhibiting abundant stretches of 6 amino acids or longer that are perfect repetitions in the reference family. We provide a systematic quantification for this repetitiveness. We show that this form of repetitiveness is not exclusive of repeat proteins, but also occurs in globular domains. A by-product of this work is a fast quantification of the likelihood of a protein to belong to a family.Fil: Turjanski, Pablo Guillermo. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Computación; ArgentinaFil: Parra, Rodrigo Gonzalo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; ArgentinaFil: Espada, Rocío. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; ArgentinaFil: Becher, Veronica Andrea. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Computación; ArgentinaFil: Ferreiro, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentin

A First-Principles Study of Zinc Oxide Honeycomb Structures

We present a first-principles study of the atomic, electronic, and magnetic properties of two-dimensional (2D), single and bilayer ZnO in honeycomb structure and its armchair and zigzag nanoribbons. In order to reveal the dimensionality effects, our study includes also bulk ZnO in wurtzite, zincblende, and hexagonal structures. The stability of 2D ZnO, its nanoribbons and flakes are analyzed by phonon frequency, as well as by finite temperature ab initio molecular-dynamics calculations. 2D ZnO in honeycomb structure and its armchair nanoribbons are nonmagnetic semiconductors but acquire net magnetic moment upon the creation of zinc-vacancy defect. Zigzag ZnO nanoribbons are ferromagnetic metals with spins localized at the oxygen atoms at the edges and have high spin polarization at the Fermi level. However, they change to nonmagnetic metal upon termination of their edges with hydrogen atoms. From the phonon calculations, the fourth acoustical mode specified as twisting mode is also revealed for armchair nanoribbon. Under tensile stress the nanoribbons are deformed elastically maintaining honeycomblike structure but yield at high strains. Beyond yielding point honeycomblike structure undergo a structural change and deform plastically by forming large polygons. The variation in the electronic and magnetic properties of these nanoribbons have been examined under strain. It appears that plastically deformed nanoribbons may offer a new class of materials with diverse properties.Comment: http://prb.aps.org/abstract/PRB/v80/i23/e23511

Unfolding first-principles band structures

A general method is presented to unfold band structures of first-principles super-cell calculations with proper spectral weight, allowing easier visualization of the electronic structure and the degree of broken translational symmetry. The resulting unfolded band structures contain additional rich information from the Kohn-Sham orbitals, and absorb the structure factor that makes them ideal for a direct comparison with angular resolved photoemission spectroscopy experiments. With negligible computational expense via the use of Wannier functions, this simple method has great practical value in the studies of a wide range of materials containing impurities, vacancies, lattice distortions, or spontaneous long-range orders.Comment: 4 pages, 3 figure

Semiclassical Universe from First Principles

Causal Dynamical Triangulations in four dimensions provide a background-independent definition of the sum over space-time geometries in nonperturbative quantum gravity. We show that the macroscopic four-dimensional world which emerges in the Euclidean sector of this theory is a bounce which satisfies a semiclassical equation. After integrating out all degrees of freedom except for a global scale factor, we obtain the ground state wave function of the universe as a function of this scale factor.Comment: 15 pages, 4 figure