First-principles calculation of alloy scattering in GexSi1-x

First-principles electronic structure methods are used to find the rates of intravalley and intervalley n-type carrier scattering due to alloy disorder in Si1-xGex alloys. The required alloy scattering matrix elements are calculated from the energy splitting of nearly degenerate Bloch states which arises when one average host atom is replaced by a Ge or Si atom in supercells containing up to 128 atoms. Scattering parameters for all relevant Delta and L intravalley and intervalley alloy scattering are calculated. Atomic relaxation is found to have a substantial effect on the scattering parameters. f-type intervalley scattering between Delta valleys is found to be comparable to other scattering channels. The n-type carrier mobility, calculated from the scattering rate using the Boltzmann transport equation in the relaxation time approximation, is in excellent agreement with experiments on bulk, unstrained alloys.

A first principles analysis of the effect of hydrogen concentration in hydrogenated amorphous silicon on the formation of strained Si-Si bonds and the optical and mobility gaps

In this paper, we use a model of hydrogenated amorphous silicon generated from molecular dynamics with density functional theory calculations to examine how the atomic geometry and the optical and mobility gaps are influenced by mild hydrogen oversaturation. The optical and mobility gaps show a volcano curve as the hydrogen content varies from undersaturation to mild oversaturation, with largest gaps obtained at the saturation hydrogen concentration. At the same time, mid-gap states associated with dangling bonds and strained Si-Si bonds disappear at saturation but reappear at mild oversaturation, which is consistent with the evolution of optical gap. The distribution of Si-Si bond distances provides the key to the change in electronic properties. In the undersaturation regime, the new electronic states in the gap arise from the presence of dangling bonds and strained Si-Si bonds, which are longer than the equilibrium Si-Si distance. Increasing hydrogen concentration up to saturation reduces the strained bonds and removes dangling bonds. In the case of mild oversaturation, the mid-gap states arise exclusively from an increase in the density of strained Si-Si bonds. Analysis of our structure shows that the extra hydrogen atoms form a bridge between neighbouring silicon atoms, thus increasing the Si-Si distance and increasing disorder in the sample.

First-Principles Study of the Electronic and Magnetic Properties of Defects in Carbon Nanostructures

Understanding the magnetic properties of graphenic nanostructures is instrumental in future spintronics applications. These magnetic properties are known to depend crucially on the presence of defects. Here we review our recent theoretical studies using density functional calculations on two types of defects in carbon nanostructures: Substitutional doping with transition metals, and sp$^3$-type defects created by covalent functionalization with organic and inorganic molecules. We focus on such defects because they can be used to create and control magnetism in graphene-based materials. Our main results are summarized as follows: i)Substitutional metal impurities are fully understood using a model based on the hybridization between the $d$ states of the metal atom and the defect levels associated with an unreconstructed D$_{3h}$ carbon vacancy. We identify three different regimes, associated with the occupation of distinct hybridization levels, which determine the magnetic properties obtained with this type of doping; ii) A spin moment of 1.0 $\mu_B$ is always induced by chemical functionalization when a molecule chemisorbs on a graphene layer via a single C-C (or other weakly polar) covalent bond. The magnetic coupling between adsorbates shows a key dependence on the sublattice adsorption site. This effect is similar to that of H adsorption, however, with universal character; iii) The spin moment of substitutional metal impurities can be controlled using strain. In particular, we show that although Ni substitutionals are non-magnetic in flat and unstrained graphene, the magnetism of these defects can be activated by applying either uniaxial strain or curvature to the graphene layer. All these results provide key information about formation and control of defect-induced magnetism in graphene and related materials.

First-Principles Calculations of the Electronic and Structural Properties of GaSb

In this paper, we carried out first-principles calculations in order to investigate the structural and electronic properties of the binary compound gallium antimonide (GaSb). This theoretical study was carried out using the Density Functional Theory within the plane-wave pseudopotential method. The effects ofexchange and correlation (XC) were treated using the functional Local Density Approximation (LDA), generalized gradient approximation (GGA): Perdew–Burke–Ernzerhof (PBE), Perdew-Burke-Ernzerhof revised for solids (PBEsol), Perdew-Wang91 (PW91), revised Perdew–Burke–Ernzerhof (rPBE), Armiento–Mattson 2005 (AM05) and meta-generalized gradient approximation (meta-GGA): Tao–Perdew– Staroverov–Scuseria (TPSS) and revised Tao–Perdew–Staroverov–Scuseria (RTPSS) and modified Becke-Johnson (MBJ). We calculated the densities of state (DOS) and band structure with different XC potentials identified and compared them with the theoretical and experimental results reported in the literature. It was discovered that functional: LDA, PBEsol, AM05 and RTPSS provide the best results to calculate the lattice parameters (a) and bulk modulus (B0); while for the cohesive energy (Ecoh), functional: AM05, RTPSS and PW91 are closer to the values obtained experimentally. The MBJ, Rtpss and AM05 values found for the band gap energy is slightly underestimated with those values reported experimentally.

First-principle data-driven models for assessment of motor disorders in Parkinson’s disease

Parkinson’s disease (PD) is an increasing neurological disorder in an aging society. The motor and non-motor symptoms of PD advance with the disease progression and occur in varying frequency and duration. In order to affirm the full extent of a patient’s condition, repeated assessments are necessary to adjust medical prescription. In clinical studies, symptoms are assessed using the unified Parkinson’s disease rating scale (UPDRS). On one hand, the subjective rating using UPDRS relies on clinical expertise. On the other hand, it requires the physical presence of patients in clinics which implies high logistical costs. Another limitation of clinical assessment is that the observation in hospital may not accurately represent a patient’s situation at home. For such reasons, the practical frequency of tracking PD symptoms may under-represent the true time scale of PD fluctuations and may result in an overall inaccurate assessment. Current technologies for at-home PD treatment are based on data-driven approaches for which the interpretation and reproduction of results are problematic.  The overall objective of this thesis is to develop and evaluate unobtrusive computer methods for enabling remote monitoring of patients with PD. It investigates first-principle data-driven model based novel signal and image processing techniques for extraction of clinically useful information from audio recordings of speech (in texts read aloud) and video recordings of gait and finger-tapping motor examinations. The aim is to map between PD symptoms severities estimated using novel computer methods and the clinical ratings based on UPDRS part-III (motor examination). A web-based test battery system consisting of self-assessment of symptoms and motor function tests was previously constructed for a touch screen mobile device. A comprehensive speech framework has been developed for this device to analyze text-dependent running speech by: (1) extracting novel signal features that are able to represent PD deficits in each individual component of the speech system, (2) mapping between clinical ratings and feature estimates of speech symptom severity, and (3) classifying between UPDRS part-III severity levels using speech features and statistical machine learning tools. A novel speech processing method called cepstral separation difference showed stronger ability to classify between speech symptom severities as compared to existing features of PD speech. In the case of finger tapping, the recorded videos of rapid finger tapping examination were processed using a novel computer-vision (CV) algorithm that extracts symptom information from video-based tapping signals using motion analysis of the index-finger which incorporates a face detection module for signal calibration. This algorithm was able to discriminate between UPDRS part III severity levels of finger tapping with high classification rates. Further analysis was performed on novel CV based gait features constructed using a standard human model to discriminate between a healthy gait and a Parkinsonian gait. The findings of this study suggest that the symptom severity levels in PD can be discriminated with high accuracies by involving a combination of first-principle (features) and data-driven (classification) approaches. The processing of audio and video recordings on one hand allows remote monitoring of speech, gait and finger-tapping examinations by the clinical staff. On the other hand, the first-principles approach eases the understanding of symptom estimates for clinicians. We have demonstrated that the selected features of speech, gait and finger tapping were able to discriminate between symptom severity levels, as well as, between healthy controls and PD patients with high classification rates. The findings support suitability of these methods to be used as decision support tools in the context of PD assessment.

Breeding Latin American tigers: operational principles for rehabilitating industrial policies

Includes bibliography

First-principle studies of intermolecular and intramolecular catalysis of protonated cocaine

We have performed a series of first-principles electronic structure calculations to examine the reaction pathways and the corresponding free energy barriers for the ester hydrolysis of protonated cocaine in its chair and boat conformations. The calculated free energy barriers for the benzoyl ester hydrolysis of protonated chair cocaine are close to the corresponding barriers calculated for the benzoyl ester hydrolysis of neutral cocaine. However, the free energy barrier calculated for the methyl ester hydrolysis of protonated cocaine in its chair conformation is significantly lower than for the methyl ester hydrolysis of neutral cocaine and for the dominant pathway of the benzoyl ester hydrolysis of protonated cocaine. The significant decrease of the free energy barrier, ∼4 kcal/mol, is attributed to the intramolecular acid catalysis of the methyl ester hydrolysis of protonated cocaine, because the transition state structure is stabilized by the strong hydrogen bond between the carbonyl oxygen of the methyl ester moiety and the protonated tropane N. The relative magnitudes of the free energy barriers calculated for different pathways of the ester hydrolysis of protonated chair cocaine are consistent with the experimental kinetic data for cocaine hydrolysis under physiologic conditions. Similar intramolecular acid catalysis also occurs for the benzoyl ester hydrolysis of (protonated) boat cocaine in the physiologic condition, although the contribution of the intramolecular hydrogen bonding to transition state stabilization is negligible. Nonetheless, the predictability of the intramolecular hydrogen bonding could be useful in generating antibody-based catalysts that recruit cocaine to the boat conformation and an analog that elicited antibodies to approximate the protonated tropane N and the benzoyl O more closely than the natural boat conformer might increase the contribution from hydrogen bonding. Such a stable analog of the transition state for intramolecular catalysis of cocaine benzoyl-ester hydrolysis was synthesized and used to successfully elicit a number of anticocaine catalytic antibodies.

Understanding the structure of the first atomic contact in gold

We have studied experimentally jump-to-contact (JC) and jump-out-of-contact (JOC) phenomena in gold electrodes. JC can be observed at first contact when two metals approach each other, while JOC occurs in the last contact before breaking. When the indentation depth between the electrodes is limited to a certain value of conductance, a highly reproducible behaviour in the evolution of the conductance can be obtained for hundreds of cycles of formation and rupture. Molecular dynamics simulations of this process show how the two metallic electrodes are shaped into tips of a well-defined crystallographic structure formed through a mechanical annealing mechanism. We report a detailed analysis of the atomic configurations obtained before contact and rupture of these stable structures and obtained their conductance using first-principles quantum transport calculations. These results help us understand the values of conductance obtained experimentally in the JC and JOC phenomena and improve our understanding of atomic-sized contacts and the evolution of their structural characteristics.

First-principle density-functional calculation of the Raman spectra of BEDT-TTF

We present a first-principles density-functional calculation for the Raman spectra of a neutral BEDT-TTF molecule. Our results are in excellent agreement with experimental results. We show that a planar Structure is not a stable state of a neutral BEDT-TTF molecule. We consider three possible conformations and discuss their relation to disorder in these systems.

Bubble Growth From First Principals

We consider the simplest relevant problem in the foaming of molten plastics, the growth of a single bubble in a sea of highly viscous Newtonian fluid, and without interference from other bubbles. This simplest problem has defied accurate solution from first principles. Despite plenty of research on foaming, classical approaches from first principles have neglected the temperature rise in the surrounding fluid, and we find that this oversimplification greatly accelerates bubble growth prediction. We use a transport phenomena approach to analyze the growth of a solitary bubble, expanding under its own pressure. We consider a bubble of ideal gas growing without the accelerating contribution from mass transfer into the bubble. We explore the roles of viscous forces, fluid inertia, and viscous dissipation. We find that bubble growth depends upon the nucleus radius and nucleus pressure. We begin with a detailed examination of the classical approaches (thermodynamics without viscous heating). Our failure to fit experimental data with these classical approaches, sets up the second part of our paper, a novel exploration of the essential decelerating role of viscous heating. We explore both isothermal and adiabatic bubble expansion, and also the decelerating role of surface tension. The adiabatic analysis accounts for the slight deceleration due to the cooling of the expanding gas, which depends on gas polyatomicity. We also explore the pressure profile, and the components of the extra stress tensor, in the fluid surrounding the growing bubble. These stresses can eventually be frozen into foamed plastics. We find that our new theory compares well with measured bubble behavior.

Density functional theory study of Fe(3)Ga

First-principles scalar relativistic calculations in supercells of 16 atoms are used to represent disordered B2 ordering of Fe(3)Ga in order to observe the effect of Ga-Ga pairs on the electronic structure of this alloy. From a comparison with pure bcc Fe it is observed that the energy position and occupation of e(g) and t(2g) states are largely affected by the Ga-Ga pairs and strengthened intraplane interactions takes place. The results show that a larger hybridization of the conduction band is in the source of the magnetostriction enhancement experimentally observed in Galfenol. (C) 2011 American Institute of Physics. [doi:10.1063/1.3525609]

Functionalized adamantane: Building blocks for nanostructure self-assembly

We report first-principles calculations on the electronic and structural properties of chemically functionalized adamantane molecules, either in isolated or crystalline forms. Boron and nitrogen functionalized molecules, aza-, tetra-aza-, bora-, and tetra-bora-adamantane, were found to be very stable in terms of energetics, consistent with available experimental data. Additionally, a hypothetical molecular crystal in a zincblende structure, involving the pair tetra-bora-adamantane and tetra-aza-adamantane, was investigated. This molecular crystal presented a direct and large electronic band gap and a bulk modulus of 20 GPa. The viability of using those functionalized molecules as fundamental building blocks for nanostructure self-assembly is discussed.

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.

Electronic properties and hyperfine fields of nickel-related complexes in diamond

We carried out a first-principles investigation on the microscopic properties of nickel-related defect centers in diamond. Several configurations, involving substitutional and interstitial nickel impurities, have been considered either in isolated configurations or forming complexes with other defects, such as vacancies and boron and nitrogen dopants. The results, in terms of spin, symmetry, and hyperfine fields, were compared with the available experimental data on electrically active centers in synthetic diamond. Several microscopic models, previously proposed to explain those data, have been confirmed by this investigation, while some models could be discarded. We also provided insights into the microscopic structure of several of those centers.

Signatures of oxygen on Cu(3)Au(100): From isolated impurity to oxide regimes

We analyze the scanning tunneling microscopy (STM) signatures for the O/Cu(3)Au(100) surface from the low-coverage (isolated impurity) to high-coverage (oxide) regimes. First-principles calculations show that oxygen signatures switch from dark to bright spots as the oxygen coverage increases. This behavior is nicely traced back to a change in the oxygen orbital character of the Fermi-level electronic states. Our results allow for the chemical identification by STM of oxygen and copper atoms in the fully ordered O/Cu(3)Au(100)-c(2x2) surface.