Ab initio two-dimensional multiband low-energy models of EtMe_3Sb[Pd(dmit)_2]_2 and \kappa-(BEDT-TTF)_2Cu(NCS)_2 with comparisons to single-band models

We present ab initio two-dimensional extended Hubbard-type multiband models for EtMe_3Sb[Pd(dmit)_2]_2 and \kappa-(BEDT-TTF)_2Cu(NCS)_2, after a downfolding scheme based on the constrained random phase approximation (cRPA) and maximally-localized Wannier orbitals, together with the dimensional downfolding. In the Pd(dmit)_2 salt, the antibonding state of the highest occupied molecular orbital (HOMO) and the bonding/antibonding states of the lowest unoccupied molecular orbital (LUMO) are considered as the orbital degrees of freedom, while, in the \kappa-BEDT-TTF salt, the HOMO-antibonding/bonding states are considered. Accordingly, a three-band model for the Pd(dmit)_2 salt and a two-band model for the \kappa-(BEDT-TTF) salt are derived. We derive single band models for the HOMO-antibonding state for both of the compounds as well.Comment: 10 pages, 9 figures, 3 tables; submitted to Physical Review

Ab initio GW plus cumulant calculation for isolated band systems: Application to organic conductor (TMTSF)2PF6 and transition-metal oxide SrVO3

We present ab initio GW plus cumulant-expansion calculations for an organic compound (TMTSF)2PF6 and a transition-metal oxide SrVO3. These materials exhibit characteristic low-energy band structures around the Fermi level, which bring about interesting low-energy properties; the low-energy bands near the Fermi level are isolated from the other bands, and, in the isolated bands, unusually low-energy plasmon excitations occur. To study the effect of this low-energy-plasmon fluctuation on the electronic structure, we calculate spectral functions and photoemission spectra using the ab initio cumulant expansion of the Green’s function based on the GW self-energy. We found that the low-energy plasmon fluctuation leads to an appreciable renormalization of the low-energy bands and a transfer of the spectral weight into the incoherent part, thus resulting in an agreement with experimental photoemission data

Optical Absorption Study by Ab initio Downfolding Approach: Application to GaAs

We examine whether essence and quantitative aspects of electronic excitation spectra are correctly captured by an effective low-energy model constructed from an {\em ab initio} downfolding scheme. A global electronic structure is first calculated by {\em ab initio} density-functional calculations with the generalized gradient approximation. With the help of constrained density functional theory, the low-energy effective Hamiltonian for bands near the Fermi level is constructed by the downfolding procedure in the basis of maximally localized Wannier functions. The excited states of this low-energy effective Hamiltonian ascribed to an extended Hubbard model are calculated by using a low-energy solver. As the solver, we employ the Hartree-Fock approximation supplemented by the single-excitation configuration-interaction method considering electron-hole interactions. The present three-stage method is applied to GaAs, where eight bands are retained in the effective model after the downfolding. The resulting spectra well reproduce the experimental results, indicating that our downfolding scheme offers a satisfactory framework of the electronic structure calculation, particularly for the excitations and dynamics as well as for the ground state.Comment: 14 pages, 6 figures, and 1 tabl

Ab initio Derivation of Low-Energy Model for κ-ET Type Organic Conductors

We derive effective Hubbard-type Hamiltonians of κ-(BEDT-TTF) 2 X, using an ab initio downfolding technique, for the first time for organic conductors. They contain dispersions of the highest occupied Wannier-type molecular orbitals with the nearest neighbor transfer t ∼0.067 eV for a metal X =Cu (NCS) 2 and 0.055 eV for a Mott insulator X =Cu 2 (CN) 3, as well as screened Coulomb interactions. It shows unexpected differences from the conventional extended Hückel results, especially much stronger onsite interaction U ∼0.8 eV (U / t ∼12–15) than the Hückel estimates (U /t ∼7–8) as well as an appreciable longer-ranged interaction. Reexamination on physics of this family of materials is required from this realistic basis

Single-molecular real-time deep sequencing reveals the dynamics of multi-drug resistant haplotypes and structural variations in the hepatitis C virus genome

While direct-acting antivirals (DAAs) for hepatitis C virus (HCV) have dramatically progressed, patients still suffer from treatment failures. For the radical eradication of HCV, a deeper understanding of multiple resistance-associated substitutions (RASs) at the single-clone level is essential. To understand HCV quasispecies and their dynamics during DAA treatment, we applied single-molecule real-time (SMRT) deep sequencing on sera from 12 patients with genotype-1b HCV infections with DAA treatment failures, both pre- and post-treatment. We identified >3.2 kbp sequences between NS3 and NS5A genes of 187, 539 clones in total, classifying into haplotype codes based on the linkage of seven RAS loci. The number of haplotype codes during the treatment, per sample, significantly decreased from 14.67 ± 9.12 to 6.58 ± 7.1, while the number of nonsynonymous codons on the seven RAS loci, per clone, significantly increased from 1.50 ± 0.92 to 3.64 ± 0.75. In five cases, the minority multi-drug resistant haplotypes at pre-treatment were identical to the major haplotypes at relapse. Moreover, various structural variations (SVs) were detected and their dynamics analysed. These results suggest that SMRT deep sequencing is useful for detecting minority haplotypes and SVs, and to evaluate the dynamics of viral genomes at the single-clone level