Ab-initio determination of x-ray absorption near edge structure (xanes) spectra in an ultrasoft and norm conserving pseudopotentials scheme

X-ray absorption spectroscopy (XAS) is a powerful means of investigation of structural and electronic properties in condensed -matter physics. Analysis of the near edge part of the XAS spectrum, the so – called X-ray Absorption Near Edge Structure (XANES), can typically provide the following information on the photoexcited atom: - Oxidation state and coordination environment. - Speciation of transition metal compounds. - Conduction band DOS projected on the excited atomic species (PDOS). Analysis of XANES spectra is greatly aided by simulations; in the most common scheme the multiple scattering framework is used with the muffin tin approximation for the scattering potential and the spectral simulation is based on a hypothetical, reference structure. This approach has the advantage of requiring relatively little computing power but in many cases the assumed structure is quite different from the actual system measured and the muffin tin approximation is not adequate for low symmetry structures or highly directional bonds. It is therefore very interesting and justified to develop alternative methods. In one approach, the spectral simulation is based on atomic coordinates obtained from a DFT (Density Functional Theory) optimized structure. In another approach, which is the object of this thesis, the XANES spectrum is calculated directly based on an ab – initio DFT calculation of the atomic and electronic structure. This method takes full advantage of the real many-electron final wavefunction that can be computed with DFT algorithms that include a core-hole in the absorbing atom to compute the final cross section. To calculate the many-electron final wavefunction the Projector Augmented Wave method (PAW) is used. In this scheme, the absorption cross section is written in function of several contributions as the many-electrons function of the finale state; it is calculated starting from pseudo-wavefunction and performing a reconstruction of the real-wavefunction by using a transform operator which contains some parameters, called partial waves and projector waves. The aim of my thesis is to apply and test the PAW methodology to the calculation of the XANES cross section. I have focused on iron and silicon structures and on some biological molecules target (myoglobin and cytochrome c). Finally other inorganic and biological systems could be taken into account for future applications of this methodology, which could become an important improvement with respect to the multiscattering approach.

Competition and cooperation between antiferrodistortive and ferroelectric instabilities in the model perovskite SrTiO₃

We use density functional theory to explore the interplay between octahedral rotations and ferroelectricity in the model compound SrTiO3. We find that over the experimentally relevant range octahedral rotations suppress ferroelectricity as is generally assumed in the literature. Somewhat surprisingly, we observe that at larger angles the previously weakened ferroelectric instability strengthens significantly. By analyzing geometry changes, energetics, force constants and charges, we explain the mechanisms behind this transition from competition to cooperation with increasing octahedral rotation angle.

Can model Hamiltonians describe the electron–electron interaction in π-conjugated systems?: PAH and graphene

Model Hamiltonians have been, and still are, a valuable tool for investigating the electronic structure of systems for which mean field theories work poorly. This review will concentrate on the application of Pariser–Parr–Pople (PPP) and Hubbard Hamiltonians to investigate some relevant properties of polycyclic aromatic hydrocarbons (PAH) and graphene. When presenting these two Hamiltonians we will resort to second quantisation which, although not the way chosen in its original proposal of the former, is much clearer. We will not attempt to be comprehensive, but rather our objective will be to try to provide the reader with information on what kinds of problems they will encounter and what tools they will need to solve them. One of the key issues concerning model Hamiltonians that will be treated in detail is the choice of model parameters. Although model Hamiltonians reduce the complexity of the original Hamiltonian, they cannot be solved in most cases exactly. So, we shall first consider the Hartree–Fock approximation, still the only tool for handling large systems, besides density functional theory (DFT) approaches. We proceed by discussing to what extent one may exactly solve model Hamiltonians and the Lanczos approach. We shall describe the configuration interaction (CI) method, a common technology in quantum chemistry but one rarely used to solve model Hamiltonians. In particular, we propose a variant of the Lanczos method, inspired by CI, that has the novelty of using as the seed of the Lanczos process a mean field (Hartree–Fock) determinant (the method will be named LCI). Two questions of interest related to model Hamiltonians will be discussed: (i) when including long-range interactions, how crucial is including in the Hamiltonian the electronic charge that compensates ion charges? (ii) Is it possible to reduce a Hamiltonian incorporating Coulomb interactions (PPP) to an 'effective' Hamiltonian including only on-site interactions (Hubbard)? The performance of CI will be checked on small molecules. The electronic structure of azulene and fused azulene will be used to illustrate several aspects of the method. As regards graphene, several questions will be considered: (i) paramagnetic versus antiferromagnetic solutions, (ii) forbidden gap versus dot size, (iii) graphene nano-ribbons, and (iv) optical properties.

5,6-Dihydroxyindole-2-carboxylic acid: a first principles density functional study

We report first principles density functional calculations for 5,6-dihydroxyindole-2-carboxylic acid (DHICA) and several oxidised forms. DHICA and 5,6-dihydroxyindole (DHI) are believed to be the basic building blocks of the eumelanins. Our results show that carboxylation has a significant effect on the physical properties of the molecules. In particular, the relative stabilities and the highest occupied molecular orbital-lowest unoccupied molecular orbital gaps (calculated with the DeltaSCF method) of the various redox forms are strongly affected. We predict that, in contrast to DHI, the density of unpaired electrons, and hence the ESR signal, in DHICA is negligibly small. (C) 2004 Elsevier B.V. All rights reserved.

Chemical and structural disorder in eumelanins: A possible explanation for broadband absorbance

We report the results of an experimental and theoretical study of the electronic and structural properties of a key eumelanin precursor-5,6,-dihydroxyindole-2-carboxylic acid ( DHICA) - and its dimeric forms. We have used optical spectroscopy to follow the oxidative polymerization of DHICA to eumelanin and observe red shifting and broadening of the absorption spectrum as the reaction proceeds. First principles density functional theory calculations indicate that DHICA oligomers ( possible reaction products of oxidative polymerization) have the gap between the highest occupied molecular orbital and the lowest unoccupied molecular orbital red-shifted gaps with respect to the monomer. Furthermore, different bonding configurations ( leading to oligomers with different structures) produce a range of gaps. These experimental and theoretical results lend support to the chemical disorder model where the broadband monotonic absorption characteristic of all melanins is a consequence of the superposition of a large number of nonhomogeneously broadened Gaussian transitions associated with each of the components of a melanin ensemble. These results suggest that the traditional model of eumelanin as an amorphous organic semiconductor is not required to explain its optical properties and should be thoroughly reexamined. These results have significant implications for our understanding of the physics, chemistry, and biological function of these important biological macromolecules. Indeed, one may speculate that the robust functionality of melanins in vitro is a direct consequence of its heterogeneity, i.e., chemical disorder is a "low cost" natural resource in these systems

A deep learning model via thermodynamics and condensed matter physics

Deep Learning architectures give brilliant results in a large variety of fields, but a comprehensive theoretical description of their inner functioning is still lacking. In this work, we try to understand the behavior of neural networks by modelling in the frameworks of Thermodynamics and Condensed Matter Physics. We approach neural networks as in a real laboratory and we measure the frequency spectrum and the entropy of the weights of the trained model. The stochasticity of the training occupies a central role in the dynamics of the weights and makes it difficult to assimilate neural networks to simple physical systems. However, the analogy with Thermodynamics and the introduction of a well defined temperature leads us to an interesting result: if we eliminate from a CNN the "hottest" filters, the performance of the model remains the same, whereas, if we eliminate the "coldest" ones, the performance gets drastically worst. This result could be exploited in the realization of a training loop which eliminates the filters that do not contribute to loss reduction. In this way, the computational cost of the training will be lightened and more importantly this would be done by following a physical model. In any case, beside important practical applications, our analysis proves that a new and improved modeling of Deep Learning systems can pave the way to new and more efficient algorithms.

Species Fractionation In Atomic Chains From Mechanically Stretched Alloys.

Bettini et al (2006 Nat. Nanotechnol. 1 182-5) reported the first experimental realization of linear atomic chains (LACs) composed of different atoms (Au and Ag). The different contents of Au and Ag were observed in the chains from what was found in the bulk alloys, which raises the question of what the wire composition is, if it is in equilibrium with a bulk alloy. In this work we address the thermodynamic driving force for species fractionation in LACs under tension, and we present the density-functional theory results for Ag-Au chain alloys. A pronounced stabilization of the wires with an alternating Ag-Au sequence is observed, which could be behind the experimentally observed Au enrichment in LACs from alloys with high Ag content.

Anomalous thermodynamic properties in ferropericlase throughout its spin crossover transition

The thermodynamics properties of ferropericlase (Mg(1-x)Fe(x)O where x=0.1875) (Fp) throughout its spin crossover were investigated by first principles. Fp was treated as an ideal solid solution of pure high-spin and low-spin states. The Gibbs free energies of the pure states were addressed using the LDA+U method. A vibrational virtual-crystal model was developed to address the vibrational properties of the pure spin cases and used in conjunction with quasiharmonic theory to compute their vibrational free energies. The thermodynamics properties of Fp display significant anomalies that should be typical of spin crossover systems in general. In Fp, in particular, they are fundamental for understanding the state of earth's interior, where the pressure and temperature conditions of the crossover are realized.

Bilayer graphene dual-gate nanodevice: An ab initio simulation

We study the electronic transport properties of a dual-gated bilayer graphene nanodevice via first-principles calculations. We investigate the electric current as a function of gate length and temperature. Under the action of an external electrical field we show that even for gate lengths up 100 angstrom, a nonzero current is exhibited. The results can be explained by the presence of a tunneling regime due the remanescent states in the gap. We also discuss the conditions to reach the charge neutrality point in a system free of defects and extrinsic carrier doping.

Unraveling effects of disorder on the electronic structure of SiO(2) from first principles

We present a first-principles systematic study of the electronic structure of SiO(2) including the crystalline polymorphs alpha quartz and beta cristobalite, and different types of disorder leading to the amorphous phase. We start from calculations within density functional theory and proceed to more sophisticated quasiparticle calculations according to the GW scheme. Our results show that different origins of disorder have also different impact on atomic and electronic-density fluctuations, which affect the electronic structure and, in particular, the size of the mobility gap in each case.

Accurate prediction of the Si/SiO(2) interface band offset using the self-consistent ab initio DFT/LDA-1/2 method

We use the density functional theory/local-density approximation (DFT/LDA)-1/2 method [L. G. Ferreira , Phys. Rev. B 78, 125116 (2008)], which attempts to fix the electron self-energy deficiency of DFT/LDA by half-ionizing the whole Bloch band of the crystal, to calculate the band offsets of two Si/SiO(2) interface models. Our results are similar to those obtained with a ""state-of-the-art"" GW approach [R. Shaltaf , Phys. Rev. Lett. 100, 186401 (2008)], with the advantage of being as computationally inexpensive as the usual DFT/LDA. Our band gap and band offset predictions are in excellent agreement with experiments.

Barrier-free substitutional doping of graphene sheets with boron atoms: Ab initio calculations

Using ab initio methods, we propose a simple and effective way to substitutionally dope graphene sheets with boron. The method consists of selectively exposing each side of the graphene sheet to different elements. We first expose one side of the membrane to boron while the other side is exposed to nitrogen. Proceeding this way, the B atoms will be spontaneously incorporated into the graphene membrane without any activation barrier. In a second step, the system should be exposed to a H-rich environment, which will remove the CN radical from the layer and form HCN, leading to a perfect substitutional doping.

Atomistic molecular dynamics study of interface formation: Al on poly(p-phenylene vinylene)

We model interface formation by metal deposition on the conjugated polymer poly-para-phenylene vinylene, studying direct aluminum and layered aluminum-calcium structures Al/PPV and Al/Ca/PPV. To do that we use classical molecular dynamics simulations, checked by ab initio density-functional theory calculations, for selected relevant configurations. We find that Al not only migrates easily into the film, with a strong charge transfer to the neighboring chains, but also promotes rearrangement of the polymer in the interfacial region to the hexagonal structure. On the other hand, our results indicate that a thin Ca layer is sufficient to protect the film and maintain a well-defined metal/polymer interface, and that also a thin Al capping layer may protect the whole from environmental degradation.

Defect-induced effects on carrier migration through one-dimensional poly(para-phenylenevinylene) chains

Defects in one-dimensional (1D) systems can be intrinsically distinct from its three-dimensional counterparts, and polymer films are good candidates for showing both extremes that are difficult to individuate in the experimental data. We study theoretically the impact of simple hydrogen and oxygen defects on the electron transport properties of one-dimensional poly(para-phenylenevinylene) chains through a multiscale technique, starting from classical structural simulations for crystalline films to extensive ab initio calculations within density functional theory for the defects in single crystalline-constrained chains. The most disruptive effect on carrier transport comes from conjugation breaking imposed by the overcoordination of a carbon atom in the vinyl group independently from the chemical nature of the defect. The particular case of the [C=O] (keto-defect) shows in addition unexpected electron-hole separation, suggesting that the experimentally detected photoluminescence bleaching and photoconductivity enhancement could be due to exciton dissociation caused by the 1D characteristics of the defect.

Contribution of the second Landau level to the exchange energy of the three-dimensional electron gas in a high magnetic field

We derive a closed analytical expression for the exchange energy of the three-dimensional interacting electron gas in strong magnetic fields, which goes beyond the quantum limit (L=0) by explicitly including the effect of the second, L=1, Landau level and arbitrary spin polarization. The inclusion of the L=1 level brings the fields to which the formula applies closer to the laboratory range, as compared to previous expressions, valid only for L=0 and complete spin polarization. We identify and explain two distinct regimes separated by a critical density n(c). Below n(c), the per particle exchange energy is lowered by the contribution of L=1, whereas above n(c) it is increased. As special cases of our general equation we recover various known more limited results for higher fields, and we identify and correct a few inconsistencies in some of these earlier expressions.