• Bulletin of the Korean Chemical Society
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• v.33 no.11
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• pp.3719-3726
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• 2012

Formation of Z-DNA, a left-handed double helix, from B-DNA, the canonical right-handed double helix, occurs during important biological processes such as gene expression and DNA transcription. Such B-Z transitions can also be induced by high salt concentration in vitro, but the changes in the relative stability of B-DNA and Z-DNA with salt concentration have not been fully explained despite numerous attempts. For example, electrostatic effects alone could not account for salt-induced B-Z transitions in previous studies. In this paper, we propose that the B-Z transition can be explained if counterion entropy is considered along with the electrostatic interactions. This can be achieved by conducting all-atom, explicit-solvent MD simulations followed by MM-PBSA and molecular DFT calculations. Our MD simulations show that counterions tend to bind at specific sites in B-DNA and Z-DNA, and that more ions cluster near Z-DNA than near B-DNA. Moreover, the difference in counterion ordering near B-DNA and Z-DNA is larger at a low salt concentration than at a high concentration. The results imply that the exclusion of counterions by Z-DNA-binding proteins may facilitate Z-DNA formation under physiological conditions.

• Bulletin of the Korean Chemical Society
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• v.27 no.7
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• pp.1071-1074
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• 2006

• Progress in Superconductivity and Cryogenics
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• v.25 no.4
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• pp.14-18
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• 2023

We have investigated the behavior induced by Ga substitution in B-1212 system and observed an anomalous superconductor-like resistivity drop with an onset near 260 K and an offset at 248 K in the nominal (B_0.65Ga_0.35)(Ba_1.25Sr_0.75)(Er_0.5Ca_0.5)Cu₂O_z compound. However, this property degraded with repeated cycling. Systematic studies of the superconducting properties of the (B_1-xGa_x)(Ba_1.25Sr_0.75)(Er_0.5Ca_0.5)Cu₂O_z compounds are reported and discussed in the context of the anomalous resistivity transition.

• Journal of the Korean Magnetic Resonance Society
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• v.21 no.3
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• pp.90-95
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• 2017

The Z-DNA domain of human ADAR1 ($Z{\alpha}_{ADAR1}$) produces B-Z junction DNA through preferential binding to the CG-repeat segment and destabilizing the neighboring AT-rich region. However, this study could not answer the question of how many base-pairs in AT-rich region are destabilized by binding of $Z{\alpha}_{ADAR1}$. Thus, we have performed NMR experiments of $Z{\alpha}_{ADAR1}$ to the longer DNA duplex containing an 8-base-paired (8-bp) CG-repeat segment and a 12-bp AT-rich region. This study revealed that $Z{\alpha}_{ADAR1}$ preferentially binds to the CG-repeat segment rather than AT-rich region in a long DNA and then destabilizes at least 6 base-pairs in the neighboring AT-rich region for efficient B-Z transition of the CG-repeat segment.

• Proceedings of the Korean Magnestics Society Conference
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• 2011.12a
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• pp.155-155
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• 2011

• Journal of the Korean Chemical Society
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• v.50 no.4
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• pp.291-297
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• 2006

The equilibrium structures, relative energies and NBO analyses for the possible conformations and transition states which can exist on the internal rotation of CPDFB and CPCFB molecules have been investigated using DFT and ab initio methods with various basis sets. The interaction between bonding orbital ((C1-C3, C2-C3)) and antibonding orbital (n*(B9) and *(B9-Cl11)) was the main characteristic hyperconjugation in both molecules. In addition, the stabilization energy of CPDFB was 6.63kcal/mol and that of CPCFB was 6.97(E-form)/6.79(Z-form) kcal/mol for each conformation. The rotational barriers by internal rotation of BF2- and BFCl- functional groups were evaluated to be 5.3~6.7kcal/mol and 5.7~6.5kcal/mol respectively, which showed good agreement with the experimental values reported by previous dynamic NMR study. Finally, Z-form was more stable than E-form by 0.2 kcal/mol in CPCFB molecule and therefore Z-form was confirmed as global minimum.

• Journal of Magnetics
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• v.16 no.2
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• pp.192-195
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• 2011

The phase transition of vortex matter from solid to liquid was studied in iron-based superconductors. Based on the traditional vortex glass theory, we have examined the magnetoresistivity data of iron-based superconductors using our extended thermal activation model: $\rho(B,T)=\rho((T-T_g(B))/(T_c(0)-T_g(B)))^{v(z-1)}$. We predict that the magnetic field-dependent area S + $S_0$ which integrates $\rho$ with T is proportional to $B^{\beta}$, where ${\beta}$ is the vortex glass transition exponent. From our calculation, the vortex glass transition exponent is 0.33, close to the exponent of area $S_0$ + S is 0.31 in $SmO_{0.9}F_{0.1}FeAs$; the exponent of area S is 0.63, which is close to the irreversibility line exponent 2/3. Both of the results show the validity of our model. In addition, our model is shown to be effective in describing irreversibility behavior in layered superconductors.

• Journal of the Korean Physical Society
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• v.73 no.9
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• pp.1370-1376
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• 2018

The electronic structures, magnetic properties and half-metallicity in $Zr_2RuZ$ (Z = Ga, In, Tl, Ge, Sn, and Pb) alloys with $AlCu_2Mn-$ and $CuHg_2Ti$-type structures were investigated using first-principles density functional theory (DFT) calculations. The calculations showed that $Zr_2RuIn$, $Zr_2RuTl$, $Zr_2RuSn$, and $Zr_2RuPb$ compounds with $CuHg_2Ti$-type structures were half-metallic ferromagnets with half-metallic band gaps of 0.18, 0.24, 0.22, and 0.27 eV, respectively. The half-metallicity originated from d-d and covalent hybridizations between the transition metals Zr and Ru. The total magnetic moments of the $Zr_2RuZ$ (Z = In, Tl, Sn, and Pb) compounds with $CuHg_2Ti$-type structures were integer values of $1{\mu}B$ and $2{\mu}B$, which is in agreement with Slater-Pauling rule ($M_{tot}=Z_{tot}-18$). Among these compounds, $Zr_2RuIn$ and $Zr_2RuTl$ were half-metals over relatively wide regions of the lattice constants, indicating that these two new Heusler alloys are ideal candidates for use in spintronic devices.

• Bulletin of the Korean Chemical Society
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• v.29 no.6
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• pp.1149-1156
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• 2008

The conformational study on neutral and zwitterionic L-alanines (N-Ala and Z-Ala, respectively) and the transition state (TS) for their interconversion is carried out using ab initio HF and density functional B3LYP methods with the self-consistent reaction field method in the gas phase and in solution. At both the HF and B3LYP levels of theory, the local minimum N1 for N-Ala is found to be most preferred in the gas phase and a weak asymmetric bifurcated hydrogen bond between the amino hydrogens and the carbonyl oxygen appears to play a role in stabilizing this conformation. The local minima N2a and N2b are found to be the second preferred conformations, which seem to be stabilized by a hydrogen bond between the amino nitrogen and the carboxylic hydrogen. The relative stability of the local minimum N2b is remarkably increased in solution than that in the gas phase. The local minimum N2b becomes more stable than the local minimum N2a in most of the solution. On the whole the relative free energies of Z-Ala and TS become more lowered, as the solvent polarity increases. N-Ala prevails over Z-Ala in aprotic solutions but Z-Ala is dominantly populated in ethanol and water. In aprotic solutions, the population of Z-Ala increases somewhat with the increase of solvent polarity. The barrier to Z-Ala-to-N-Ala interconversion increases on the whole with the increase of solvent polarity, which is caused by the increase of stability for Z-Ala.

• The Journal of the Institute of Internet, Broadcasting and Communication
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• v.10 no.4
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• pp.169-176
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• 2010

We propose a Z-HBT line coding for a LED-ID system. Z-HBT line coding is defined as follows. First, we apply half bit transition to one bit. Second, we decode encoded bits using difference of bit transition level in one bit duration. As a result, we obtain advantages about synchronization problem and noise effect mitigation at the receiver. We set up outdoor the LED-ID simulation environment. At simulation results, we show 2-3dB gain as compared with existing line coding schemes. The results of the paper can be applied to design and implementation of LED-ID systems for indoor wireless multimedia services.