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Park, Dongbin,Goh, Chul Jun,Kim, Hyein,Hahn, Yoonsoo The Korean Society of Plant Pathology 2018 Plant Pathology Journal Vol.34 No.2
The genome sequences of two novel monopartite RNA viruses were identified in a common eelgrass (Zostera marina) transcriptome dataset. Sequence comparison and phylogenetic analyses revealed that these two novel viruses belong to the genus Amalgavirus in the family Amalgaviridae. They were named Zostera marina amalgavirus 1 (ZmAV1) and Zostera marina amalgavirus 2 (ZmAV2). Genomes of both ZmAV1 and ZmAV2 contain two overlapping open reading frames (ORFs). ORF1 encodes a putative replication factory matrix-like protein, while ORF2 encodes a RNA-dependent RNA polymerase (RdRp) domain. The fusion protein (ORF1+2) of ORF1 and ORF2, which mediates RNA replication, was produced using the +1 programmed ribosomal frameshifting (PRF) mechanism. The +1 PRF motif sequence, UUU_CGN, which is highly conserved among known amalgaviruses, was also found in ZmAV1 and ZmAV2. Multiple sequence alignment of the ORF1+2 fusion proteins from 24 amalgaviruses revealed that +1 PRF occurred only at three different positions within the 13-amino acid-long segment, which was surrounded by highly conserved regions on both sides. This suggested that the +1 PRF may be constrained by the structure of fusion proteins. Genome sequences of ZmAV1 and ZmAV2, which are the first viruses to be identified in common eelgrass, will serve as useful resources for studying evolution and diversity of amalgaviruses.
( Dongbin Park ),( Yoonsoo Hahn ) 한국미생물생명공학회(구 한국산업미생물학회) 2017 Journal of microbiology and biotechnology Vol.27 No.7
Complete genome sequences of three new plant RNA viruses, Spinach deltapartitivirus 1 (SpDPV1), Spinach amalgavirus 1 (SpAV1), and Spinach latent virus (SpLV), were identified from a spinach (Spinacia oleracea) transcriptome dataset. The RNA-dependent RNA polymerases (RdRps) of SpDPV1, SpAV1, and SpLV showed 72%, 53%, and 93% amino acid sequence identities with the homologous RdRp of the most closely related virus, respectively, suggesting that SpDPV1 and SpAV1 were novel viruses. Sequence similarity and phylogenetic analyses revealed that SpDPV1 belonged to the genus Deltapartitivirus of the family Partitiviridae, SpAV1 to the genus Amalgavirus of the family Amalgaviridae, and SpLV to the genus Ilarvirus of the family Bromoviridae. Based on the demarcation criteria, SpDPV1 and SpAV1 are considered as novel species of the genera Deltapartitivirus and Amalgavirus, respectively. This is the first report of these two viruses from spinach.
( Dongbin Park ),( Yoonsoo Hahn ) 한국미생물 · 생명공학회 2017 Journal of microbiology and biotechnology Vol.27 No.4
A distinct double-stranded RNA (dsRNA) cryptic virus, named spinach cryptic virus 1 (SpCV1), was identified from spinach transcriptome datasets. The SpCV1 genome has two dsRNA genome segments. The larger dsRNA1 has an open reading frame for a conserved RNA-dependent RNA polymerase (RdRp). The smaller dsRNA2 encodes a putative coat protein (CP). The sequence identity of SpCV1 RdRp and CP to the closest cryptic virus is 81% and 60%, respectively. Phylogenetic analysis indicates that SpCV1 is a novel member of the genus Alphapartitivirus (family Partitiviridae).
Shin, Dongbin,Lee, Geunsik,Miyamoto, Youshiyuki,Park, Noejung American Chemical Society 2016 Journal of chemical theory and computation Vol.12 No.1
<P>We present methods for combining time-dependent density functional theory and the Hubbard U potential in the framework of the real-time propagation of Kohn-Sham orbitals to describe electron-atom coupled dynamics beyond the Born-Oppenheimer approximation. The time evolution of the non-commuting nonlocal operators were realized through Crank-Nicolson's inversion method and Suzuki-Trotter's split exponentiation. The electron dynamics related to the high speed motion of an alkali atom on a conjugated carbon plane is presented. The nonequilibrium charge oscillation between a metal surface and a localized atomic orbital, as modeled with graphene and Ca, is discussed.</P>
Unraveling materials Berry curvature and Chern numbers from real-time evolution of Bloch states
Shin, Dongbin,Sato, Shunsuke A.,Hü,bener, Hannes,De Giovannini, Umberto,Kim, Jeongwoo,Park, Noejung,Rubio, Angel National Academy of Sciences 2019 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.116 No.10
<▼1><P><B>Significance</B></P><P>It was established by Thouless, Kohmoto, Nightingale, and den Nijs in 1982 that the topology of the solid-state wavefunctions leads to quantization of transverse electrical conductivity of an insulator. This recognition has led to the development of the new field of topological materials characterized by symmetry-protected quantum numbers. Here, we propose a general and computationally efficient framework enabling one to unveil and predict materials-topological invariants in terms of physical observables, such as the bulk time-dependent current. We show how the quantized charge and spin Hall effect appears even for materials with a non-Abelian Berry phase. This dynamical approach is not necessarily restricted to density functional theory, but can be extended to other schemes and to other methods dealing with correlations explicitly.</P></▼1><▼2><P>Materials can be classified by the topological character of their electronic structure and, in this perspective, global attributes immune to local deformations have been discussed in terms of Berry curvature and Chern numbers. Except for instructional simple models, linear response theories have been ubiquitously used in calculations of topological properties of real materials. Here we propose a completely different and versatile approach to obtain the topological characteristics of materials by calculating physical observables from the real-time evolving Bloch states: The cell-averaged current density reveals the anomalous velocities that lead to the conductivity quantum. Results for prototypical cases are shown, including a spin-frozen valley Hall and a quantum anomalous Hall insulator. The advantage of this method is best illustrated by the example of a quantum spin Hall insulator: The quantized spin Hall conductivity is straightforwardly obtained irrespective of the non-Abelian nature in its Berry curvature. Moreover, the method can be extended to the description of real observables in nonequilibrium states of topological materials.</P></▼2>
Atomically resolved orientational ordering of C60 molecules on epitaxial graphene on Cu(111).
Jung, Minbok,Shin, Dongbin,Sohn, So-Dam,Kwon, Soon-Yong,Park, Noejung,Shin, Hyung-Joon RSC Pub 2014 Nanoscale Vol.6 No.20
<P>A detailed understanding of interactions between molecules and graphene is one of the key issues for tailoring the properties of graphene-based molecular devices, because the electronic and structural properties of molecular layers on surfaces are determined by intermolecular and molecule-substrate interactions. Here, we present the atomically resolved experimental measurements of the self-assembled fullerene molecules on single-layer graphene on Cu(111). Fullerene molecules form a (4 4) superstructure on graphene/Cu(111), revealing only single molecular orientation. We can resolve the exact adsorption site and the configuration of fullerene by means of low-temperature scanning tunnelling microscopy (LT-STM) and density functional theory (DFT) calculations. The adsorption orientation can be explained in terms of the competition between intermolecular interactions and molecule-substrate interactions, where strong Coulomb interactions among the fullerenes determine the in-plane orientation of the fullerene. Our results provide important implications for developing carbon-based organic devices using a graphene template in the future.</P>