Chebyshev polynomial filtered subspace iteration in the Discontinuous Galerkin method for large-scale electronic structure calculations

The Discontinuous Galerkin (DG) electronic structure method employs an adaptive local basis (ALB) set to solve the Kohn-Sham equations of density functional theory (DFT) in a discontinuous Galerkin framework. The adaptive local basis is generated on-the-fly to capture the local material physics, and can systematically attain chemical accuracy with only a few tens of degrees of freedom per atom. A central issue for large-scale calculations, however, is the computation of the electron density (and subsequently, ground state properties) from the discretized Hamiltonian in an efficient and scalable manner. We show in this work how Chebyshev polynomial filtered subspace iteration (CheFSI) can be used to address this issue and push the envelope in large-scale materials simulations in a discontinuous Galerkin framework. We describe how the subspace filtering steps can be performed in an efficient and scalable manner using a two-dimensional parallelization scheme, thanks to the orthogonality of the DG basis set and block-sparse structure of the DG Hamiltonian matrix. The on-the-fly nature of the ALBs requires additional care in carrying out the subspace iterations. We demonstrate the parallel scalability of the DG-CheFSI approach in calculations of large-scale two-dimensional graphene sheets and bulk three-dimensional lithium-ion electrolyte systems. Employing 55,296 computational cores, the time per self-consistent field iteration for a sample of the bulk 3D electrolyte containing 8,586 atoms is 90 seconds, and the time for a graphene sheet containing 11,520 atoms is 75 seconds.Comment: Submitted to The Journal of Chemical Physic

A global study for acute myeloid leukemia with RARG rearrangement

Acute myeloid leukemia (AML) with retinoic acid receptor γ (RARG) rearrangement has clinical, morphologic, and immunophenotypic features similar to classic acute promyelocytic leukemia. However, AML with RARG rearrangement is insensitive to alltrans retinoic acid (ATRA) and arsenic trioxide (ATO) and carries a poor prognosis. We initiated a global cooperative study to define the clinicopathological features, genomic and transcriptomic landscape, and outcomes of AML with RARG rearrangements collected from 29 study groups/institutions worldwide. Thirty-four patients with AML with RARG rearrangements were identified. Bleeding or ecchymosis was present in 18 (54.5%) patients. Morphology diagnosed as M3 and M3v accounted for 73.5% and 26.5% of the cases, respectively. Immunophenotyping showed the following characteristics: positive for CD33, CD13, and MPO but negative for CD38, CD11b, CD34, and HLA-DR. Cytogenetics showed normal karyotype in 38% and t(11;12) in 26% of patients. The partner genes of RARG were diverse and included CPSF6, NUP98, HNRNPc, HNRNPm, PML, and NPM1. WT1- and NRAS/KRAS-mutations were common comutations. None of the 34 patients responded to ATRA and/or ATO. Death within 45 days from diagnosis occurred in 10 patients (∼29%). At the last follow-up, 23 patients had died, and the estimated 2-year cumulative incidence of relapse, event-free survival, and overall survival were 68.7%, 26.7%, and 33.5%, respectively. Unsupervised hierarchical clustering using RNA sequencing data from 201 patients with AML showed that 81.8% of the RARG fusion samples clustered together, suggesting a new molecular subtype. RARG rearrangement is a novel entity of AML that confers a poor prognosis. This study is registered with the Chinese Clinical Trial Registry (ChiCTR2200055810)

What Makes a Better Annuity?

The wide gulf between actual and predicted annuity demand has been well documented. However, a comparable gap exists between the current and ideal annuity market. In a world with costly and limited annuity products, we investigate what types of new annuity products could improve annuity market participation and increase individual welfare. We find that participation gains are most likely for new annuity products that focus on late-life payouts which offer a large price discount relative to their financial market analogues. For example, the marginal utility from the first dollar allocated to a late-life annuity can be several times that of an immediate annuity. Our welfare analysis indicates that an individual’s current assets suggest desirable new annuity products since annuities that lower the cost of the existing consumption plan necessarily improve welfare. Finally, we consider the implications for annuity demand if new annuity products ultimately complete the annuity market. Given access to a complete market, we find all individuals only purchase annuity contracts with a significant time gap between purchase and payout. At a minimum, enough time must pass between purchase and payout to build up a mortality discount sufficient to overcome the cost of creating the contract. Since most existing annuity products, such as immediate annuities, do not have this feature, few current annuity contract configurations are likely to survive significant product innovation. Taken together, our results indicate that there is ample opportunity for innovation to spur annuity demand and improve individual welfare

Decoherent Scattering of Light Particles in a D-Brane Background

We discuss the scattering of two light particles in a D-brane background. It is known that, if one light particle strikes the D brane at small impact parameter, quantum recoil effects induce entanglement entropy in both the excited D brane and the scattered particle. In this paper we compute the asymptotic `out' state of a second light particle scattering off the D brane at large impact parameter, showing that it also becomes mixed as a consequence of quantum D-brane recoil effects. We interpret this as a non-factorizing contribution to the superscattering operator S-dollar for the two light particles in a Liouville D-brane background, that appears when quantum D-brane excitations are taken into account.Comment: 18 pages LATEX, one figure (incorporated

A novel polymer of tubulin forms the conoid of Toxoplasma gondii

Toxoplasma gondii is an obligatory intracellular parasite, an important human pathogen, and a convenient laboratory model for many other human and veterinary pathogens in the phylum Apicomplexa, such as Plasmodium, Eimeria, and Cryptosporidia. 22 subpellicular microtubules form a scaffold that defines the cell shape of T. gondii. Its cytoskeleton also includes an intricate apical structure consisting of the conoid, two intraconoid microtubules, and two polar rings. The conoid is a 380-nm diameter motile organelle, consisting of fibers wound into a spiral like a compressed spring. FRAP analysis of transgenic T. gondii expressing YFP-α-tubulin reveals that the conoid fibers are assembled by rapid incorporation of tubulin subunits during early, but not late, stages of cell division. Electron microscopic analysis shows that in the mature conoid, tubulin is arranged into a novel polymer form that is quite different from typical microtubules

Cryptic photosynthesis, Extrasolar planetary oxygen without a surface biological signature

On the Earth, photosynthetic organisms are responsible for the production of virtually all of the oxygen in the atmosphere. On the land, vegetation reflects in the visible, leading to a red edge that developed about 450 Myr ago and has been proposed as a biosignature for life on extrasolar planets. However, in many regions of the Earth, and particularly where surface conditions are extreme, for example in hot and cold deserts, photosynthetic organisms can be driven into and under substrates where light is still sufficient for photosynthesis. These communities exhibit no detectable surface spectral signature to indicate life. The same is true of the assemblages of photosynthetic organisms at more than a few metres depth in water bodies. These communities are widespread and dominate local photosynthetic productivity. We review known cryptic photosynthetic communities and their productivity. We link geomicrobiology with observational astronomy by calculating the disk-averaged spectra of cryptic habitats and identifying detectable features on an exoplanet dominated by such a biota. The hypothetical cryptic photosynthesis worlds discussed here are Earth-analogs that show detectable atmospheric biomarkers like our own planet, but do not exhibit a discernable biological surface feature in the disc-averaged spectrum.Comment: 23 pages, 2 figures, Astrobiology (TBP) - updated Table 1, typo in detectable O2 correcte