First-Principles Study of Structure, Vibrational, and Elastic Properties of Stoichiometric and Calcium-Deficient Hydroxyapatite

Hydroxyapatite (HAp), a primary constituent of human bone, is usually nonstoichiometric with varying Ca/P molar ratios, with the well-known fact that Ca deficiency can cause marked reductions in its mechanical properties. To gain insights into the mechanism of this degradation, we employ first-principles calculations based on density functional theory and determine the effects of Ca deficiency on structure, vibrational, and elastic properties of HAp. Our simulation results confirm a considerable reduction in the elastic constants of HAp due to Ca deficiency, which was experimentally reported earlier. Stress-induced transformation of the Ca-deficient defected structure into a metastable state upon the application of stress could be a reason for this. Local structural stability of HAp and Ca-deficient HAp structures is assessed with full phonon dispersion studies. Further, specific signatures in the computed vibrational spectra for Ca deficiency in HAp can be utilized in experimental characterization of different types of defected HAp.

Temperature-dependent stability of stacking faults in Al, Cu and Ni: first-principles analysis

We present comparative analysis of microscopic mechanisms relevant to plastic deformation of the face-centered cubic (FCC) metals Al, Cu, and Ni, through determination of the temperature-dependent free energies of intrinsic and unstable stacking faults along 1 (1) over bar 0] and 1 (2) over bar 1] on the (1 1 1) plane using first-principles density-functional-theory-based calculations. We show that vibrational contribution results in significant decrease in the free energy of barriers and intrinsic stacking faults (ISFs) of Al, Cu, and Ni with temperature, confirming an important role of thermal fluctuations in the stability of stacking faults (SFs) and deformation at elevated temperatures. In contrast to Al and Ni, the vibrational spectrum of the unstable stacking fault (USF1 (2) over bar 1]) in Cu reveals structural instabilities, indicating that the energy barrier (gamma(usf)) along the (1 1 1)1 (2) over bar 1] slip system in Cu, determined by typical first-principles calculations, is an overestimate, and its commonly used interpretation as the energy release rate needed for dislocation nucleation, as proposed by Rice (1992 J. Mech. Phys. Solids 40 239), should be taken with caution.

Elastic Properties Of Sulphur And Selenium Doped Ternary PbTe Alloys By First Principles

Lead telluride (PbTe) is an established thermoelectric material which can be alloyed with sulphur and selenium to further enhance the thermoelectric properties. Here, a first principles study of ternary alloys PbSxTe(1-x) and PbSexTe(1-x) (0 <= x <= 1) based on the Virtual Crystal Approximation (VCA) is presented for different ratios of the isoelectronic atoms in each series. Equilibrium lattice parameters and elastic constants have been calculated and compared with the reported data. Anisotropy parameter calculated from the stiffness constants showed a slight improvement in anisotropy of elastic properties of the alloys over undoped PbTe. Furthermore, the alloys satisfied the predicted stability criteria from the elastic constants, showing stable structures, which agreed with the previously reported experimental results.

First principles study of metal contacts to monolayer black phosphorous

Atomically thin layered black phosphorous (BP) has recently appeared as an alternative to the transitional metal dichalcogenides for future channel material in a metal-oxide-semiconductor transistor due to its lower carrier effective mass. Investigation of the electronic property of source/drain contact involving metal and two-dimensional material is essential as it impacts the transistor performance. In this paper, we perform a systematic and rigorous study to evaluate the Ohmic nature of the side-contact formed by the monolayer BP (mBP) and metals (gold, titanium, and palladium), which are commonly used in experiments. Employing the Density Functional Theory, we analyse the potential barrier, charge transfer and atomic orbital overlap at the metal-mBP interface in an optimized structure to understand how efficiently carriers could be injected from metal contact to the mBP channel. Our analysis shows that gold forms a Schottky contact with a higher tunnel barrier at the interface in comparison to the titanium and palladium. mBP contact with palladium is found to be purely Ohmic, where as titanium contact demonstrates an intermediate behaviour. (C) 2014 AIP Publishing LLC.

First-Principles Study on Structural Stability of Belite

A first-principles study was carried out to investigate the stability of the crystal structure of beta-form belite (beta-C2S) substituted by Sr atoms as trace impurities for Ca atoms in CaOx polyhedra. The effect of the connection types of CaOx polyhedral, in the form of common-edge bond and common-face bond, upon the crystal stability is described. The Ca-Ca interatomic distance closely relates to the hydraulic activity of beta-C2S. The beta-C2S substituted by an Sr atom for Ca(1) atoms having seven Ca-O bonds is energetically more stable than that substituted by an Sr atom for Ca(2) atoms having eight Ca-O bonds. The Sr-doped beta-C2S having a common face bond with SrOx polyhedra is energetically more favorable and results in structural stability compared with that having a common edge bond with SrOx polyhedra.

Effect of oxygen vacancies on the elastic properties of zinc oxide: A first-principles investigation

The effect of oxygen vacancies on the elastic properties of zinc oxide (ZnO) is examined using first-principles calculations based on density functional theory. Formation energies of vacancies in different types of oxygen deficient structures were analyzed to ascertain their stability. This analysis reveals that the doubly-charged oxygen vacancy under zinc-rich growth conditions is the most stable. Results show considerable degradation of some of the elastic moduli due to the presence of oxygen vacancies, which is in agreement with recent experiments. The decrease observed in elastic constants is more pronounced with increase in vacancy concentration. Further, the charge state of the defect structure was found to influence the shear elastic constants. Evaluation of elastic anisotropy of stoichiometric and oxygen deficient ZnO indicates the significant anisotropy in elastic properties and stiff c-axis orientation. (C) 2014 Elsevier B.V. All rights reserved.

First principles study of structural stability and site preference in Co-3 (W,X)

Since the discovery 1] of gamma' precipitate (L1(2) - Co-3 (Al, W)) in the Co-Al-W ternary system, there has been an increased interest in Co-based superalloys. Since these alloys have two phase microstructures (gamma + gamma') similar to Ni-based superalloys 2], they are viable candidates in high temperature applications, particularly in land-based turbines. The role of alloying on stability of the gamma' phase has been an active area of research. In this study, electronic structure calculations were done to probe the effect of alloying in Co3W with L1(2) structure. Compositions of type Co-3(W, X), (where X/Y = Mn, Fe, Ni, Pt, Cr, Al, Si, V, W, Ta, Ti, Nb, Hf, Zr and Mo) were studied. Effect of alloying on equilibrium lattice parameters and ground state energies was used to calculate Vegard's coefficients and site preference related data. The effect of alloying on the stability of the L1(2) structure vis a vis other geometrically close packed ordered structures was also studied for a range of Co3X compounds. Results suggest that the penchant of element for the W sublattice can be predicted by comparing heats of formation of Co3X in different structures.

First-principles study of the influence of different interfaces and core types on the properties of CdSe/CdS core-shell nanocrystals

With the expanding field of nanoengineering and the production of nanocrystals (NCs) with higher quality and tunable size, having reliable theoretical calculations to complement the experimental results is very important. Here we present such a study of CdSe/CdS core-shell NCs using density functional theory, where we focus on dependence of the properties of these NCs on core types and interfaces between the core and the shell, as well as on the core/shell ratio. We show that the density of states and the absorption indices depend rather weakly on the type of interface and core type. We demonstrate that the HOMO wavefunction is mainly localised in the core of the nanocrystal, depending primarily on the core/shell ratio. On the other hand the LUMO wavefunction spreads more into the shell of the nanocrystal, where its confinement in the core is almost the same in each of the studied structural models. Furthermore, we show that the radiative lifetimes decrease with increasing core sizes due to changes in the dipolar overlap integral of the HOMO and LUMO wavefunctions. In addition, the electron-hole Coulomb interaction energies follow a similar pattern as the localisation of the wavefunctions, with the smaller NCs having higher Coulomb interaction energies.

Pressure-induced structural phase transitions and phonon anomalies in ReO3: Raman and first-principles study

We report high-pressure Raman-scattering studies on single-crystal ReO3 up to 26.9 GPa at room temperature, complemented by first-principles density functional calculations to assign the modes and to develop understanding of the subtle features of the low-pressure phase transition. The pressure (P) dependence of phonon frequencies (omega) reveals three phase transitions at 0.6, 3, and 12.5 GPa with characteristic splitting and changes in the slope of omega(P). Our first-principles theoretical analysis confirms the role of the rotational modes of ReO6, M-3, to the lowest pressure structural transition, and shows that the transition from the Pm3m to the Im3 structure is a weak first-order transition, originating from the strong anharmonic coupling of the M-3 modes with the acoustic modes (strain).

Design of symmetric TIM barrel proteins from first principles

Background: Computational protein design is a rapidly maturing field within structural biology, with the goal of designing proteins with custom structures and functions. Such proteins could find widespread medical and industrial applications. Here, we have adapted algorithms from the Rosetta software suite to design much larger proteins, based on ideal geometric and topological criteria. Furthermore, we have developed techniques to incorporate symmetry into designed structures. For our first design attempt, we targeted the (alpha/beta)(8) TIM barrel scaffold. We gained novel insights into TIM barrel folding mechanisms from studying natural TIM barrel structures, and from analyzing previous TIM barrel design attempts. Methods: Computational protein design and analysis was performed using the Rosetta software suite and custom scripts. Genes encoding all designed proteins were synthesized and cloned on the pET20-b vector. Standard circular dichroism and gel chromatographic experiments were performed to determine protein biophysical characteristics. 1D NMR and 2D HSQC experiments were performed to determine protein structural characteristics. Results: Extensive protein design simulations coupled with ab initio modeling yielded several all-atom models of ideal, 4-fold symmetric TIM barrels. Four such models were experimentally characterized. The best designed structure (Symmetrin-1) contained a polar, histidine-rich pore, forming an extensive hydrogen bonding network. Symmetrin-1 was easily expressed and readily soluble. It showed circular dichroism spectra characteristic of well-folded alpha/beta proteins. Temperature melting experiments revealed cooperative and reversible unfolding, with a T-m of 44 degrees C and a Gibbs free energy of unfolding (Delta G degrees) of 8.0 kJ/mol. Urea denaturing experiments confirmed these observations, revealing a C-m of 1.6 M and a Delta G degrees of 8.3 kJ/mol. Symmetrin-1 adopted a monomeric conformation, with an apparent molecular weight of 32.12 kDa, and displayed well resolved 1D-NMR spectra. However, the HSQC spectrum revealed somewhat molten characteristics. Conclusions: Despite the detection of molten characteristics, the creation of a soluble, cooperatively folding protein represents an advancement over previous attempts at TIM barrel design. Strategies to further improve Symmetrin-1 are elaborated. Our techniques may be used to create other large, internally symmetric proteins.

First principles DFT investigation Of Yttrium-decorated Boron-Nitride Nanotube: Electronic Structure and Hydrogen Storage

The electronic structure and hydrogen storage capability of Yttrium-doped BNNTs has been theoretically investigated using first principles density functional theory (DFT). Yttrium atom prefers the hollow site in the center of the hexagonal ring with a binding energy of 0.8048eV. Decorating by Y makes the system half-metallic and magnetic with a magnetic moment of 1.0 mu(B). Y decorated Boron-Nitride (8,0) nanotube can adsorb up to five hydrogen molecules whose average binding energy is computed as 0.5044eV. All the hydrogen molecules are adsorbed with an average desorption temperature of 644.708 K. Taking that the Y atoms can be placed only in alternate hexagons, the implied wt% comes out to be 5.31%, a relatively acceptable value for hydrogen storage materials. Thus, this system can serve as potential hydrogen storage medium.

High temperature thermoelectric properties of Zr and Hf based transition metal dichalcogenides: A first principles study

We investigate the electronic and thermal transport properties of bulk MX2 compounds (M = Zr, Hf and X = S, Se) by first-principles calculations and semi-classical Boltzmann transport theory. The band structure shows the confinement of heavy and light bands along the out of plane and in-plane directions, respectively. This results in high electrical conductivity (sigma) and large thermopower leading to a high power factor (S-2 sigma) for moderate n-type doping. The phonon dispersion demonstrates low frequency flat acoustical modes, which results in low group velocities (v(g)). Consequently, lowering the lattice thermal conductivity (kappa(latt)) below 2 W/m K. Low kappa(latt) combined with high power factor results in ZT > 0.8 for all the bulk MX2 compounds at high temperature of 1200 K. In particular, the ZT(max) of HfSe2 exceeds 1 at 1400 K. Our results show that Hf/Zr based dichalcogenides are very promising for high temperature thermoelectric application. (C) 2015 AIP Publishing LLC.

First-principles study of the electronic and magnetic properties of defective carbon nanostructures

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First-principles study of the electronic structure and dynamical electronic excitations of strong spin-orbit metal Pb: bulk, surface and nanosized films

En la presente tesis se ha realizado el estudio de primeros principios (esto es, sinhacer uso de parámetros ajustables) de la estructura electrónica y la dinámica deexcitaciones electrónicas en plomo, tanto en volumen como en superficie y en formade películas de espesor nanométrico. Al presentar el plomo un número atómico alto(82), deben tenerse en cuenta los efectos relativistas. Con este fin, el doctorando haimplementado el acoplo espín-órbita en los códigos computacionales que hanrepresentado la principal herramienta de trabajo.En volumen, se han encontrado fuertes efectos relativistas asi como de lalocalización de los electrones, tanto en la respuesta dieléctrica (excitacioneselectrónicas colectivas) como en el tiempo de vida de electrones excitados. Lacomparación de nuestros resultados con medidas experimentales ha ayudado aprofundizar en dichos efectos.En el estudio de las películas a escala nanométrica se han hallado fuertes efectoscuánticos debido al confinamiento de los estados electrónicos. Dichos efectos semanifiestan tanto en el estado fundamental (en acuerdo con estudiosexperimentales), como en la respuesta dieléctrica a través de la aparición y dinámicade plasmones de diversas características. Los efectos relativistas, a pesar de no serimportantes en la estructura electrónica de las películas, son los responsables de ladesaparación del plasmón de baja energía en nuestros resultados.

First principles based multiparadigm modeling of electronic structures and dynamics

Electronic structures and dynamics are the key to linking the material composition and structure to functionality and performance.

An essential issue in developing semiconductor devices for photovoltaics is to design materials with optimal band gaps and relative positioning of band levels. Approximate DFT methods have been justified to predict band gaps from KS/GKS eigenvalues, but the accuracy is decisively dependent on the choice of XC functionals. We show here for CuInSe₂ and CuGaSe₂, the parent compounds of the promising CIGS solar cells, conventional LDA and GGA obtain gaps of 0.0-0.01 and 0.02-0.24 eV (versus experimental values of 1.04 and 1.67 eV), while the historically first global hybrid functional, B3PW91, is surprisingly the best, with band gaps of 1.07 and 1.58 eV. Furthermore, we show that for 27 related binary and ternary semiconductors, B3PW91 predicts gaps with a MAD of only 0.09 eV, which is substantially better than all modern hybrid functionals, including B3LYP (MAD of 0.19 eV) and screened hybrid functional HSE06 (MAD of 0.18 eV).

The laboratory performance of CIGS solar cells (> 20% efficiency) makes them promising candidate photovoltaic devices. However, there remains little understanding of how defects at the CIGS/CdS interface affect the band offsets and interfacial energies, and hence the performance of manufactured devices. To determine these relationships, we use the B3PW91 hybrid functional of DFT with the AEP method that we validate to provide very accurate descriptions of both band gaps and band offsets. This confirms the weak dependence of band offsets on surface orientation observed experimentally. We predict that the CBO of perfect CuInSe₂/CdS interface is large, 0.79 eV, which would dramatically degrade performance. Moreover we show that band gap widening induced by Ga adjusts only the VBO, and we find that Cd impurities do not significantly affect the CBO. Thus we show that Cu vacancies at the interface play the key role in enabling the tunability of CBO. We predict that Na further improves the CBO through electrostatically elevating the valence levels to decrease the CBO, explaining the observed essential role of Na for high performance. Moreover we find that K leads to a dramatic decrease in the CBO to 0.05 eV, much better than Na. We suggest that the efficiency of CIGS devices might be improved substantially by tuning the ratio of Na to K, with the improved phase stability of Na balancing phase instability from K. All these defects reduce interfacial stability slightly, but not significantly.

A number of exotic structures have been formed through high pressure chemistry, but applications have been hindered by difficulties in recovering the high pressure phase to ambient conditions (i.e., one atmosphere and room temperature). Here we use dispersion-corrected DFT (PBE-ulg flavor) to predict that above 60 GPa the most stable form of N₂O (the laughing gas in its molecular form) is a 1D polymer with an all-nitrogen backbone analogous to cis-polyacetylene in which alternate N are bonded (ionic covalent) to O. The analogous trans-polymer is only 0.03-0.10 eV/molecular unit less stable. Upon relaxation to ambient conditions both polymers relax below 14 GPa to the same stable non-planar trans-polymer, accompanied by possible electronic structure transitions. The predicted phonon spectrum and dissociation kinetics validate the stability of this trans-poly-NNO at ambient conditions, which has potential applications as a new type of conducting polymer with all-nitrogen chains and as a high-energy oxidizer for rocket propulsion. This work illustrates in silico materials discovery particularly in the realm of extreme conditions.

Modeling non-adiabatic electron dynamics has been a long-standing challenge for computational chemistry and materials science, and the eFF method presents a cost-efficient alternative. However, due to the deficiency of FSG representation, eFF is limited to low-Z elements with electrons of predominant s-character. To overcome this, we introduce a formal set of ECP extensions that enable accurate description of p-block elements. The extensions consist of a model representing the core electrons with the nucleus as a single pseudo particle represented by FSG, interacting with valence electrons through ECPs. We demonstrate and validate the ECP extensions for complex bonding structures, geometries, and energetics of systems with p-block character (C, O, Al, Si) and apply them to study materials under extreme mechanical loading conditions.

Despite its success, the eFF framework has some limitations, originated from both the design of Pauli potentials and the FSG representation. To overcome these, we develop a new framework of two-level hierarchy that is a more rigorous and accurate successor to the eFF method. The fundamental level, GHA-QM, is based on a new set of Pauli potentials that renders exact QM level of accuracy for any FSG represented electron systems. To achieve this, we start with using exactly derived energy expressions for the same spin electron pair, and fitting a simple functional form, inspired by DFT, against open singlet electron pair curves (H₂ systems). Symmetric and asymmetric scaling factors are then introduced at this level to recover the QM total energies of multiple electron pair systems from the sum of local interactions. To complement the imperfect FSG representation, the AMPERE extension is implemented, and aims at embedding the interactions associated with both the cusp condition and explicit nodal structures. The whole GHA-QM+AMPERE framework is tested on H element, and the preliminary results are promising.