ADEPT: a domain independent sequence alignment strategy for gpu architectures.

Background: Bioinformatic workflows frequently make use of automated genome assembly and protein clustering tools. At the core of most of these tools, a significant portion of execution time is spent in determining optimal local alignment between two sequences. This task is performed with the Smith-Waterman algorithm, which is a dynamic programming based method.

Exascale applications: skin in the game.

As noted in Wikipedia, refers to having 'incurred risk by being involved in achieving a goal', where ' is a synecdoche for the person involved, and is the metaphor for actions on the field of play under discussion'. For exascale applications under development in the US Department of Energy Exascale Computing Project, nothing could be more apt, with the being exascale applications and the being delivering comprehensive science-based computational applications that effectively exploit exascale high-performance computing technologies to provide breakthrough modelling and simulation and data science solutions. These solutions will yield high-confidence insights and answers to the most critical problems and challenges for the USA in scientific discovery, national security, energy assurance, economic competitiveness and advanced healthcare.

GW100: Benchmarking G0W0 for Molecular Systems.

We present the GW100 set. GW100 is a benchmark set of the ionization potentials and electron affinities of 100 molecules computed with the GW method using three independent GW codes and different GW methodologies. The quasi-particle energies of the highest-occupied molecular orbitals (HOMO) and lowest-unoccupied molecular orbitals (LUMO) are calculated for the GW100 set at the G0W0@PBE level using the software packages TURBOMOLE, FHI-aims, and BerkeleyGW.

An explicit formula for optical oscillator strength of excitons in semiconducting single-walled carbon nanotubes: family behavior.

The sensitive structural dependence of the optical properties of single-walled carbon nanotubes, which are dominated by excitons and tunable by changing diameter and chirality, makes them excellent candidates for optical devices. Because of strong many-electron interaction effects, the detailed dependence of the optical oscillator strength f(s) of excitons on nanotube diameter d, chiral angle θ, and electronic subband index P (the so-called family behavior), however, has been unclear. In this study, based on results from an extended Hubbard Hamiltonian with parameters derived from ab initio GW plus Bethe-Salpeter equation (GW-BSE) calculations, we have obtained an explicit formula for the family behavior of the oscillator strengths of excitons in semiconducting single-walled carbon nanotubes (SWCNTs), incorporating environmental screening.

First-principles calculations of quasiparticle excitations of open-shell condensed matter systems.

We develop a Green's function approach to quasiparticle excitations of open-shell systems within the GW approximation. It is shown that accurate calculations of the characteristic multiplet structure require a precise knowledge of the self-energy and, in particular, its poles. We achieve this by constructing the self-energy from appropriately chosen mean-field theories on a fine frequency grid.

An atlas of carbon nanotube optical transitions.

Electron-electron interactions are significantly enhanced in one-dimensional systems, and single-walled carbon nanotubes provide a unique opportunity for studying such interactions and the related many-body effects in one dimension. However, single-walled nanotubes can have a wide range of diameters and hundreds of different structures, each defined by its chiral index (n,m), where n and m are integers that can have values from zero up to 30 or more. Moreover, one-third of these structures are metals and two-thirds are semiconductors, and they display optical resonances at many different frequencies.

Simple approximate physical orbitals for GW quasiparticle calculations.

Generating unoccupied orbitals within density functional theory (DFT) for use in GW calculations of quasiparticle energies becomes prohibitive for large systems. We show that, without any loss of accuracy, the unoccupied orbitals may be replaced by a set of simple approximate physical orbitals made from appropriately prepared plane waves and localized basis DFT orbitals that represent the continuum and resonant states of the system, respectively. This approach allows for accurate quasiparticle calculations using only a very small number of unoccupied DFT orbitals, resulting in an order of magnitude gain in speed.

Many-body interactions in quasi-freestanding graphene.

The Landau-Fermi liquid picture for quasiparticles assumes that charge carriers are dressed by many-body interactions, forming one of the fundamental theories of solids. Whether this picture still holds for a semimetal such as graphene at the neutrality point, i.e.

Excitonic effects on the optical response of graphene and bilayer graphene.

We present first-principles calculations of many-electron effects on the optical response of graphene, bilayer graphene, and graphite employing the GW-Bethe Salpeter equation approach. We find that resonant excitons are formed in these two-dimensional semimetals. The resonant excitons give rise to a prominent peak in the absorption spectrum near 4.

Electron-hole interaction in carbon nanotubes: novel screening and exciton excitation spectra.

The optical response of single-walled carbon nanotubes is dominated by exciton states with unusually large binding energies. We show that screening in semiconducting tubes enhances rather than reduces the electron-hole interaction for separations larger than the tube diameter. This "antiscreening" region deepens the relative energy level of the higher exciton states yielding unconventional excitation spectra.

Observation of excitons in one-dimensional metallic single-walled carbon nanotubes.

Excitons are generally believed not to exist in metals because of strong screening by free carriers. Here we demonstrate that excitonic states can in fact be produced in metallic systems of a one-dimensional character. Using metallic single-walled carbon nanotubes as a model system, we show both experimentally and theoretically that electron-hole pairs form tightly bound excitons.

Bound excitons in metallic single-walled carbon nanotubes.

We extend previous ab initio calculations on excitonic effects in metallic single-walled carbon nanotubes to more experimentally realizable larger diameter tubes. Our calculations predict bound exciton states in both the (10,10) and (12,0) tubes with binding energies of approximately 50 meV providing experimentally verifiable changes to the absorption line shape in each case. The second and third van Hove singularities in the joint density of states also give rise to a single optically active bound or resonant excitonic state.