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Daejeon, South Korea

Papakonstantinou P.,Korea Basic Science Institute
Physical Review C - Nuclear Physics | Year: 2014

It has been revealed through numerical calculations that the second random phase approximation (SRPA) with the Hartree-Fock solution as its reference state results in 1. spurious states at genuinely finite energy, contrary to common expectation, and 2. unstable solutions, which within the first-order random phase approximation correspond to real low-energy collective vibrations. In the present work, these shortcomings of SRPA are shown to not contradict Thouless' theorem about the energy-weighted sum rule, and their origin is traced to the violation of the stability condition. A more general theorem is proven. Formal arguments are elucidated through numerical examples. Implications for the validity of the SRPA are discussed. © 2014 American Physical Society. Source


Thermococcus onnurineus NA1, a sulfur-reducing hyperthermophilic archaeon, is capable of H(2)-producing growth, considered to be hydrogenogenic carboxydotrophy. Utilization of formate as a sole energy source has been well studied in T. onnurineus NA1. However, whether formate can be used as its carbon source remains unknown. To obtain a global view of the metabolic characteristics of H(2)-producing growth, a quantitative proteome analysis of T. onnurineus NA1 grown on formate, CO, and starch was performed by combining one-dimensional SDS-PAGE with nano UPLC-MS(E). A total of 587 proteins corresponding to 29.7% of the encoding genes were identified, and the major metabolic pathways (especially energy metabolism) were characterized at the protein level. Expression of glycolytic enzymes was common but more highly induced in starch-grown cells. In contrast, enzymes involved in key steps of the gluconeogenesis and pentose phosphate pathways were strongly up-regulated in formate-grown cells, suggesting that formate could be utilized as a carbon source by T. onnurineus NA1. In accordance with the genomic analysis, comprehensive proteomic analysis also revealed a number of hydrogenase clusters apparently associated with formate metabolism. On the other hand, CODH and CO-induced hydrogenases belonging to the Hyg4-II cluster, as well as sulfhydrogenase-I and Mbx, were prominently expressed during CO culture. Our data suggest that CO can be utilized as a sole energy source for H(2) production via an electron transport mechanism and that CO(2) produced from catabolism or CO oxidation by CODH and CO-induced hydrogenases may subsequently be assimilated into the organic carbon. Overall, proteomic comparison of formate- and CO-grown cells with starch-grown cells revealed that a single carbon compound, such as formate and CO, can be utilized as an efficient substrate to provide cellular carbon and/or energy by T. onnurineus NA1. Source


Olsen S.L.,Korea Basic Science Institute
Frontiers of Physics | Year: 2014

QCD-motivated models for hadrons predict an assortment of “exotic” hadrons that have structures that are more complex than the quark-antiquark mesons and three-quark baryons of the original quark-parton model. These include pentaquark baryons, the six-quark H-dibaryon, and tetraquark, hybrid and glueball mesons. Despite extensive experimental searches, no unambiguous candidates for any of these exotic configurations have been identified. On the other hand, a number of meson states, one that seems to be a proton-antiproton bound state, and others that contain either charmed-anticharmed quark pairs or bottom-antibottom quark pairs, have been recently discovered that neither fit into the quark-antiquark meson picture nor match the expected properties of the QCD-inspired exotics. Here I briefly review results from a recent search for the H-dibaryon, and discuss some properties of the newly discovered states -the proton-antiproton state and the so-called XY Z mesons- and compare them with expectations for conventional quark-antiquark mesons and the predicted QCD-exotic states. © 2015, The Author(s). Source


Kim H.,Hanyang University | Kim J.-S.,Korea Basic Science Institute | Kim J.-S.,Seoul National University
Nature Reviews Genetics | Year: 2014

Programmable nucleases-including zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and RNA-guided engineered nucleases (RGENs) derived from the bacterial clustered regularly interspaced short palindromic repeat (CRISPR)-Cas (CRISPR-associated) system-enable targeted genetic modifications in cultured cells, as well as in whole animals and plants. The value of these enzymes in research, medicine and biotechnology arises from their ability to induce site-specific DNA cleavage in the genome, the repair (through endogenous mechanisms) of which allows high-precision genome editing. However, these nucleases differ in several respects, including their composition, targetable sites, specificities and mutation signatures, among other characteristics. Knowledge of nuclease-specific features, as well as of their pros and cons, is essential for researchers to choose the most appropriate tool for a range of applications. © 2014 Macmillan Publishers Limited. All rights reserved. Source


Ivanov I.A.,Korea Basic Science Institute
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2015

We describe a procedure for the solution of the time-dependent Dirac equation. The procedure is based on the relativistic generalization of the matrix iteration method. We use this procedure to study electron-momentum distribution along the laser-beam propagation direction for the process of the tunneling ionization of a hydrogen atom. We found, in agreement with the experimental observations [C. T. L. Smeenk, L. Arissian, B. Zhou, A. Mysyrowicz, D. M. Villeneuve, A. Staudte, and P. B. Corkum, Phys. Rev. Lett. 106, 193002 (2011)10.1103/PhysRevLett.106.193002], that relativistic effects lead to appreciable deviation of the distribution from the strict left-right symmetry present in the nonrelativistic case. The expectation value of the momentum along the laser-beam propagation direction grows linearly with intensity and follows closely the behavior of the expectation value of the kinetic energy divided by the speed of light. These features agree with the experimental results [C. T. L. Smeenk, L. Arissian, B. Zhou, A. Mysyrowicz, D. M. Villeneuve, A. Staudte, and P. B. Corkum, Phys. Rev. Lett. 106, 193002 (2011)10.1103/PhysRevLett.106.193002]. © 2015 American Physical Society. Source

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