Evolution of the Fermi surface of arsenic through the rhombohedral to simple-cubic phase transition: a Wannier interpolation study

The pressure dependence of the Fermi surface of arsenic is examined using the technique of Wannier interpolation, enabling a dense sampling of the Brillouin zone and the ability to capture fine features within it. Focusing primarily on the A7 to simple-cubic phase transition, we find that this semimetal to metal transition is accompanied by the folding of Fermi surfaces. The pressure dependence of the density of states (DOS) of arsenic indicates that the onset of the Peierls-type cubic to rhombohedral distortion is signified by the appearance of emerging van Hove singularities in the DOS, especially around the Fermi level. As we noted in an earlier study, high levels of convergence are consequently required for an accurate description of this transition.Comment: 19 pages, 21 figures, 16 animated gif file

Factors influencing the distribution of charge in polar nanocrystals

We perform first-principles calculations of wurtzite GaAs nanorods to explore the factors determining charge distributions in polar nanostructures. We show that both the direction and magnitude of the dipole moment $\mathbf{d}$ of a nanorod, and its electic field, depend sensitively on how its surfaces are terminated and do not depend strongly on the spontaneous polarization of the underlying lattice. We identify two physical mechanisms by which $\mathbf{d}$ is controlled by the surface termination, and we show that the excess charge on the nanorod ends is not strongly localized. We discuss the implications of these results for tuning nanocrystal properties, and for their growth and assembly.Comment: Accepted for publication in Phys. Rev. B Rapid Communication

Bromophenyl functionalization of carbon nanotubes : an ab initio study

We study the thermodynamics of bromophenyl functionalization of carbon nanotubes with respect to diameter and metallic/insulating character using density-functional theory (DFT). On one hand, we show that the activation energy for the grafting of a bromophenyl molecule onto a semiconducting zigzag nanotube ranges from 0.73 eV to 0.76 eV without any clear trend with respect to diameter within numerical accuracy. On the other hand, the binding energy of a single bromophenyl molecule shows a clear diameter dependence and ranges from 1.51 eV for a (8,0) zigzag nanotube to 0.83 eV for a (20,0) zigzag nanotube. This is in part explained by the transition from sp2 to sp3 bonding occurring to a carbon atom of a nanotube when a phenyl is grafted to it and the fact that smaller nanotubes are closer to a sp3 hybridization than larger ones due to increased curvature. Since a second bromophenyl unit can attach without energy barrier next to an isolated grafted unit, they are assumed to exist in pairs. The para configuration is found to be favored for the pairs and their binding energy decreases with increasing diameter, ranging from 4.34 eV for a (7,0) nanotube to 2.27 eV for a (29,0) nanotube. An analytic form for this radius dependence is derived using a tight binding hamiltonian and first order perturbation theory. The 1/R^2 dependance obtained (where R is the nanotube radius) is verified by our DFT results within numerical accuracy. Finally, metallic nanotubes are found to be more reactive than semiconducting nanotubes, a feature that can be explained by a non-zero density of states at the Fermi level for metallic nanotubes.Comment: 7 pages, 5 figures and 3 table

Unravelling the roles of size, ligands and pressure in the piezochromic properties of CdS nanocrystals

Understanding the effects of pressure-induced deformations on the optoelectronic properties of nanomaterials is important not only from the fundamental point of view, but also for potential applications such as stress sensors and electromechanical devices. Here we describe the novel insights into these piezochromic effects gained from using a linear-scaling density functional theory framework and an electronic enthalpy scheme, which allow us to accurately characterize the electronic structure of CdS nanocrystals with a zincblende-like core of experimentally relevant size. In particular we focus on unravelling the complex interplay of size and surface (phenyl) ligands with pressure. We show that pressure-induced deformations are not simple isotropic scaling of the original structures and that the change in HOMO-LUMO gap with pressure results from two competing factors: (i) a bulk-like linear increase due to compression, which is offset by (ii) distortions/disorder and, to a lesser extent, orbital hybridization induced by ligands affecting the frontier orbitals. Moreover, we observe that the main peak in the optical absorption spectra is systematically red-shifted or blue-shifted, as pressure is increased up to 5 GPa, depending on the presence or absence of phenyl ligands. These heavily hybridize the frontier orbitals, causing a reduction in overlap and oscillator strength, so that at zero pressure the lowest energy transition involves deeper hole orbitals than in the case of hydrogencapped nanocrystals; the application of pressure induces greater delocalisation over the whole nanocrystals bringing the frontier hole orbitals into play and resulting in an unexpected red shift for the phenyl-capped nanocrystals, in part caused by distortions. In response to a growing interest in relatively small nanocrystals that can be difficult to accurately characterize with experimental techniques, this work exemplifies the detailed understanding of structure-property relationships under pressure that can be obtained for realistic nanocrystals with state-of-the-art first principles methods and used for the characterization and design of devices based on these and similar nanomaterials

Electrostatic considerations affecting the calculated HOMO-LUMO gap in protein molecules.

A detailed study of energy differences between the highest occupied and lowest unoccupied molecular orbitals (HOMO-LUMO gaps) in protein systems and water clusters is presented. Recent work questioning the applicability of Kohn-Sham density-functional theory to proteins and large water clusters (E. Rudberg, J. Phys.: Condens. Mat. 2012, 24, 072202) has demonstrated vanishing HOMO-LUMO gaps for these systems, which is generally attributed to the treatment of exchange in the functional used. The present work shows that the vanishing gap is, in fact, an electrostatic artefact of the method used to prepare the system. Practical solutions for ensuring the gap is maintained when the system size is increased are demonstrated. This work has important implications for the use of large-scale density-functional theory in biomolecular systems, particularly in the simulation of photoemission, optical absorption and electronic transport, all of which depend critically on differences between energies of molecular orbitals.Comment: 13 pages, 4 figure

Simulations of nanocrystals under pressure : combining electronic enthalpy and linear-scaling density-functional theory

We present an implementation in a linear-scaling density-functional theory code of an electronic enthalpy method, which has been found to benatural and efficient for the ab initio calculation of finite systems underhydrostatic pressure. Based on a definition of the system volume as that enclosed within anelectronic density isosurface [M. Cococcioni, F. Mauri,G. Ceder, and N. Marzari, Phys. Rev. Lett.94, 145501 (2005)], it supports bothgeometry optimizations and molecular dynamics simulations. We introduce an approach for calibratingthe parameters defining the volume in the context of geometry optimizations and discuss theirsignificance. Results in good agreement with simulations using explicit solvents are obtained, validating ourapproach. Size-dependent pressure-induced structural transformations andvariations in the energy gap of hydrogenated silicon nanocrystals areinvestigated, including one comparable in size to recent experiments. A detailed analysis of thepolyamorphic transformationsreveals three types of amorphous structures and theirpersistence on depressurization is assessed

Toward ab initio optical spectroscopy of the Fenna-Matthews-Olson complex

We present progress toward a first-principles parametrization of the Hamiltonian of the Fenna–Matthews–Olson pigment–protein complex, a molecule that has become key to understanding the role of quantum dynamics in photosynthetic exciton energy transfer. To this end, we have performed fully quantum mechanical calculations on each of the seven bacteriochlorophyll pigments that make up the complex, including a significant proportion of their protein environment (more than 2000 atoms), using linear-scaling density functional theory exploiting a recent development for the computation of excited states. Local pigment transition energies and interpigment coupling between optical transitions have been calculated and are in good agreement with the literature consensus. Comparisons between simulated and experimental optical spectra point toward future work that may help to elucidate important design principles in these nanoscale devices

Smooth-filamental transition of active tracer fields stirred by chaotic advection

The spatial distribution of interacting chemical fields is investigated in the non-diffusive limit. The evolution of fluid parcels is described by independent dynamical systems driven by chaotic advection. The distribution can be filamental or smooth depending on the relative strength of the dispersion due to chaotic advection and the stability of the chemical dynamics. We give the condition for the smooth-filamental transition and relate the H\"older exponent of the filamental structure to the Lyapunov exponents. Theoretical findings are illustrated by numerical experiments.Comment: 4 pages, 3 figure