Systematic pseudopotentials from reference eigenvalue sets for DFT calculations

Under a Creative Commons license.-- et al.Pseudopotential-based Density-Functional Theory (DFT) permits the calculation of material properties with a modest computational effort, besides an acknowledged tradeoff of generating and testing pseudopotentials that reproduce established benchmark structural and electronic properties. To facilitate the needed benchmarking process, here we present a pragmatic method to optimize pseudopotentials for arbitrary materials directly from eigenvalue sets consistent with all-electron results. This method thus represents a much needed pragmatic route for the creation and assessment of sensitive pseudopotentials for DFT calculations that has been exemplified within the context of the SIESTA code. Comprehensive optimized pseudopotentials, basis sets, and lattice parameters are provided for twenty chemical elements in the bulk, and for both LDA and GGA exchange–correlation potentials. This method helps addressing the following issues: (i) the electronic dispersion and structural properties for Ge, Pd, Pt, Au, Ag, and Ta better agree with respect to all-electron results now, (ii) we provide the expected metallic behavior of Sn in the bulk – which comes out semiconducting when using available pseudopotentials, (iii) we create a validated pseudopotential for LDA-tungsten, and (iv) we create the first Bi pseudopotential for SIESTA that reproduces well-known electron and hole pockets at the L and T points. We investigated the transferability of these pseudopotentials and basis sets, and predict a new phase for two-dimensional tin as well.P.R. and S.B.L. acknowledge partial support from the Arkansas Biosciences Institute. V.M.G.S. and J.F. acknowledge funding from the Spanish MICINN, Grant FIS2012-34858, and European Commission FP7 ITN “MOLESCO” (Grant No. 606728). V.M.G.S. thanks the Spanish Ministerio de Economía y Competitividad for a Ramón y Cajal fellowship (RYC-2010-06053), Y.Y. and L.B. thank ONR (Grants N00014-11-1-0384 and N00014-12-1-1034), and K.P. acknowledges funding from the National Science Foundation (DMR-1206354).Peer Reviewe

From toothpaste to topological insulators and materials for valleytronics: the journeys of fluorinated tin

Resumen del trabajo presentado al American Physical Society March Meeting, celebrado en San Antonio, Texas (USA) del 2 al 6 de marzo de 2015.Tin fluoride has a vast literature. This material is stable in bulk form at room temperature and has commercial applications that include fluorinated toothpaste. Bulk tin fluoride has a pair of fluorine atoms bridging two tin atoms. In the recent past the electronic properties of 2D tin with honeycomb structure have been discussed thus generating a wealth of literature that emphasizes its non-topologically-trivial electronic properties due to the combination of a Dirac-like dispersion and a strong spin-orbit coupling given its large atomic mass. Nevertheless the stability of such freestanding structures has been contested recently. As it turns out, the most stable form of fluorinated tin does not possess a graphane-like structure either. In the most stable phase to be discussed here, fluorine atoms tilt away from (graphane-like) positions over/below tin atoms; in an atomistic arrangement similar to the one seen on their parent bulk structure. Electronic properties depend on atomistic coordination, and the most stable form of fluorinated tin does not possess non-trivial topological properties. Nevertheless it represents a new paradigm for valleytronics in 2D.Peer Reviewe

Solanum tuberosum Microtuber Development under Darkness Unveiled through RNAseq Transcriptomic Analysis

Potato microtuber (MT) development through in vitro techniques are ideal propagules for producing high quality potato plants. MT formation is influenced by several factors, i.e., photoperiod, sucrose, hormones, and osmotic stress. We have previously developed a protocol of MT induction in medium with sucrose (8% w/v), gelrite (6g/L), and 2iP as cytokinin under darkness. To understand the molecular mechanisms involved, we performed a transcriptome-wide analysis. Here we show that 1715 up- and 1624 down-regulated genes were involved in this biological process. Through the protein–protein interaction (PPI) network analyses performed in the STRING database (v11.5), we found 299 genes tightly associated in 14 clusters. Two major clusters of up-regulated proteins fundamental for life growth and development were found: 29 ribosomal proteins (RPs) interacting with 6 PEBP family members and 117 cell cycle (CC) proteins. The PPI network of up-regulated transcription factors (TFs) revealed that at least six TFs–MYB43, TSF, bZIP27, bZIP43, HAT4 and WOX9–may be involved during MTs development. The PPI network of down-regulated genes revealed a cluster of 83 proteins involved in light and photosynthesis, 110 in response to hormone, 74 in hormone mediate signaling pathway and 22 related to aging

Structural phase transition and material properties of few-layer monochalcogenides

GeSe and SnSe monochalcogenide monolayers and bilayers undergo a two-dimensional phase transition from a rectangular unit cell to a square unit cell at a critical temperature Tc well below the melting point. Its consequences on material properties are studied within the framework of Car-Parrinello molecular dynamics and density-functional theory. No in-gap states develop as the structural transition takes place, so that these phase-change materials remain semiconducting below and above Tc. As the in-plane lattice transforms from a rectangle into a square at Tc, the electronic, spin, optical, and piezoelectric properties dramatically depart from earlier predictions. Indeed, the Y and X points in the Brillouin zone become effectively equivalent at Tc, leading to a symmetric electronic structure. The spin polarization at the conduction valley edge vanishes, and the hole conductivity must display an anomalous thermal increase at Tc. The linear optical absorption band edge must change its polarization as well, making this structural and electronic evolution verifiable by optical means. Much excitement is drawn by theoretical predictions of giant piezoelectricity and ferroelectricity in these materials, and we estimate a pyroelectric response of about 3×10−12 C/Km here. These results uncover the fundamental role of temperature as a control knob for the physical properties of few-layer group-IV monochalcogenides.M. M. and S. B.-L. are funded by an Early Career Grant from the U.S. DOE (Grant No. SC0016139). Y. Y. and L. B. were funded by ONR Grant No. N00014-12-1-1034, and B. M. F. by NSF Grant No. DMR-1206515 and CONACyT (Mexico). J. F. acknowledges funding from the Spanish MICINN, Grant No. FIS2012-34858, and European Commission FP7 ITN MOLESCO (Grant No. 606728). Calculations were performed on Trestles at the Arkansas High Performance Computing Center, which is funded through multiple National Science Foundation grants and the Arkansas Economic Development Commission.Peer Reviewe