• 한국생물물리학회:학술대회논문집
• /
• 한국생물물리학회 2003년도 정기총회 및 학술발표회
• /
• pp.75-75
• /
• 2003

We report here the results on N-acetyl-N'-dimethylamide of proline (Ac-Pro-NM $e_2$) calculated using the ab initio molecular orbital method with the self-consistent reaction field (SCRF) theory at the HF level with the 6-31+G(d) basis set to investigate the conformational preference of polyproline depending on the cis/trans peptide bonds and down/up puckerings along the backbone torsion angle $\square$ in the gas phase, chloroform, and water. In the gas phase, Ac-Pro-NM $e_2$ has seven local minima of tFd, tFu, cFd, cFu, cAu, tAu, and cAd conformations. In particular, polyproline conformations tFd, tFu, cFd, and cFu are found to be more stable than $\square$-helical conformations cAu, tAu, and cAd. In contrast, Ac-Pro-NHMe has seven local minima of tCd, tCu, cBd, cAu, tAu, cFd, and cFu conformations. Conformations tCd and tCu are found to be most stable, which is ascribed to the intramolecular hydrogen bond between C=O of acetyl group and $N^{~}$ H of N'-methyl amide group. The stability of the cFd conformation (i.e., the polyproline I structure) in chloroform is somewhat increased, relative to that in water, although tFd and tFu conformations (i.e., the polyproline II structure) are dominate both in chloroform and water. The population of backbone conformations feasible in chloroform and water is consistent with the experiments. This work is supported by a Korea Research Foundation Grant (KRF-2002-041-C00129).

• Archives of Pharmacal Research
• /
• 제29권1호
• /
• pp.50-58
• /
• 2006

Translationally controlled tumor protein (TCTP), also known as histamine releasing factor (HRF), is found abundantly in different eukaryotic cell types. The sequence homology of TCTP between different species is very high, belonging to the MSS4/DSS4 superfamily of proteins. TCTP is involved in both cell growth and human late allergy reaction, as well as having a calcium binding property; however, its primary biological functions remain to be clearly elucidated. In regard to many possible functions, the TCTP of Plasmodium falciparum (Pf) is known to bind with an antimalarial agent, artemisinin, which is activated by heme. It is assumed that the endoperoxide-bridge of artemisinin is opened up by heme to form a free radical, which then eventually alkylates, probably to the Cys14 of PfTCTP. Study of the docking of artemisinin with heme, and subsequently with PfTCTP, was carried out to verify the above hypothesis on the basis of structural interactions. The three dimensional (3D) structure of PfTCTP was built by homology modeling, using the NMR structure of the TCTP of Schizosaccharomyces pombe as a template. The quality of the model was examined based on its secondary structure and biological function, as well as with the use of structure evaluating programs. The interactions between artemisinin, heme and PfTCTP were then studied using the docking program, FlexiDock. The center of the peroxide bond of artemisinin and the Fe of heme were docked within a short distance of $2.6{\AA}$, implying the strong possibility of an interaction between the two molecules, as proposed. When the activated form of artemisinin was docked on the PfTCTP, the C4-radical of the drug faced towards the sulfur of Cys14 within a distance of $2.48{\AA}$, again suggesting the possibility of alkylation having occurred. These results confirm the proposed mechanism of the antimalarial effect of artemisinin, which will provide a reliable method for establishing the mechanism of its biological activity using a molecular modeling study.

• Bulletin of the Korean Chemical Society
• /
• 제31권6호
• /
• pp.1704-1710
• /
• 2010

The structure of a 2D grid-like copper(II) complex [Cu$(NCO)_2$(pyz)](pyz=pyrazine) (1) consists of 1D chains of Cu-pyz units connected by double end-on (EO) cyanato bridges. Each Cu(II) ion has a distorted octahedral coordination, completed by the four EO cyanato and two pyrazine ligands. Magnetic interactions through EO cyanato and pyrazine bridges in 1 are discussed on the basis of DFT broken-symmetry calculations at the B3LYP level. For model dicopper(II) complexes I (bridged by cyanato) and II (bridged by pyrazine), electronic structure calculations reproduce very well the experimental couplings for the S = 1/2 ferromagnetic and antiferromagnetic exchange-coupled 2D system: the calculated exchange parameters J are +1.25 $cm^{-1}$ and -3.07 $cm^{-1}$ for I and II, respectively. The $\sigma$ orbital interactions between the Cu $x^2-y^2$ magnetic orbitals and the nitrogen lone-pair orbitals of pyrazine are analyzed from the viewpoint of through-bond interaction. The energy splitting of 0.106 eV between two SOMOs indicates that the superexchange interaction should be antiferromagnetic in II. On the other hand, there are no bridging orbitals that efficiently connect the two copper(II) magnetic orbitals in I because the HOMOs of the basal-apical NCO bridge do not play a role in the formation of overlap interaction pathway. The energy separation in the pair of SOMOs of I is calculated to be very small (0.054 eV). This result is consistent with the occurrence of weakly ferromagnetic properties in I.

• 한국전산구조공학회논문집
• /
• 제27권2호
• /
• pp.87-94
• /
• 2014

페리다이나믹 이론은 재료파괴 및 균열진전 해석에 적합하다. 그러나 적분 방정식을 풀기위해 많은 비국부 상호작용을 해석해야만 하기 때문에 일반적으로 사용되는 국부 모델들에 비해 비효율적이다. 따라서 효율적이면서 정확한 해석 모델을 구성하기 위해 페리다이나믹 모델과 다른 국부 모델을 연성하는 연성 해석법의 개발이 필요하다. 연성 방법론 개발을 위해서는 불연속성 혹은 응력 집중이 발생될 것으로 예상되는 영역에는 페리다이나믹 모델을 구성하고 상대적으로 변형 거동이 복잡하지 않은 영역은 국부 모델을 구성하는 방법이 많이 사용된다. 본 연구에서는 최근에 개발된 힘-기반 연성 방법론을 소개한다. 이 방법론에서는 블랜딩 함수를 활용하여 연성 영역을 사이에 두고 페리다이나믹 모델과 탄성체 모델을 연성한다. 수치예제를 통해 연성 모델이 집중하중 해석 혹은 정적파괴 해석 문제를 효율적이고 엄밀하게 해석할 수 있음을 확인하였다. 이와 같은 문제들은 일반적인 탄성체 모델을 사용해서는 엄밀한 해석이 어렵다. 반면에 페리다이나믹 모델은 엄밀한 해석이 가능하지만 계산 시간과 비용이 매우 많이 요구된다는 문제점이 있다.

• Smart Structures and Systems
• /
• 제17권2호
• /
• pp.297-311
• /
• 2016

Based on the distributed fiber optic sensing (DFOS) technique, plastic optical fibers (POFs) are attractive candidates to measure deformations of geotechnical structures because they can withstand large strains before rupture. Understanding the mechanical interaction between an embedded POF and the surrounding soil or rock is a necessary step towards establishing an effective POF-based sensing system for geotechnical monitoring. This paper describes a first attempt to evaluate the feasibility of POF-based soil deformation monitoring considering the POF-soil interfacial properties. A series of pullout tests were performed under various confining pressures (CPs) on a jacketed polymethyl methacrylate (PMMA) POF embedded in soil specimens. The test results were interpreted using a fiber-soil interaction model, and were compared with previous test data of silica optical fibers (SOFs). The results showed that the range of CP in this study did not induce plastic deformation of the POF; therefore, the POF-soil and the SOF-soil interfaces had similar behavior. CP was found to play an important role in controlling the fiber-soil interfacial bond and the fiber measurement range. Moreover, an expression was formulated to determine whether a POF would undergo plastic deformation when measuring soil deformation. The plasticity of POF may influence the reliability of measurements, especially for monitored geo-structures whose deformation would alternately increase and decrease. Taken together, these results indicate that in terms of the interfacial parameters studied here the POF is feasible for monitoring soil deformation as long as the plastic deformation issue is carefully addressed.

• Structural Engineering and Mechanics
• /
• 제75권6호
• /
• pp.643-657
• /
• 2020

This study presents experimental and numerical investigations on circular steel tube confined ultra high performance concrete (UHPC) columns under axial compression. The plain UHPC without fibers was designed to achieve a compressive strength ranged between 150 MPa and 200 MPa. Test results revealed that loading on only the UHPC core can generate a significant confinement effect for the UHPC core, thus leading to an increase in both strength and ductility of columns, and restricting the inherent brittleness of unconfined UHPC. All tested columns failed by shear plane failure of the UHPC core, this causes a softening stage in the axial load versus axial strain curves. In addition, an increase in the steel tube thickness or the confinement index was found to increase the strength and ductility enhancement and to reduce the magnitude of the loss of load capacity. Besides, steel tube with higher yield strength can improve the post-peak behavior. Based on the test results, the load contribution of the steel tube and the concrete core to the total load was examined. It was found that no significant confinement effect can be developed before the peak load, while the ductility of post-peak stage is mainly affected by the degree of the confinement effect. A finite element model (FEM) was also constructed in ABAQUS software to validate the test results. The effect of bond strength between the steel tube and the UHPC core was also investigated through the change of friction coefficient in FEM. Furthermore, the mechanism of circular steel tube confined UHPC columns was examined using the established FEM. Based on the results of FEM, the confining pressures along the height of each modeled column were shown. Furthermore, the interaction between the steel tube and the UHPC core was displayed through the slip length and shear stresses between two surfaces of two materials.

• 대한전자공학회논문지SD
• /
• 제41권8호
• /
• pp.1-8
• /
• 2004

두께가 3nm인 게이트 산화막을 사용한 n-MOSFET에 정전압 스트레스를 가하였을 때 관찰되는 SILC 및 soft breakdown 열화 및 이러한 열화가 소자 특성에 미치는 영향에 대해 실험하였다. 열화 현상은 인가되는 게이트 전압의 극성에 따라 그 특성이 다르게 나타났다. 게이트 전압이 (-)일 때 열화는 계면 및 산화막내 전하 결함에 의해 발생되었지만, 게이트 전압이 (＋)일 때는 열화는 주로 계면 결함에 의해 발생되었다. 또한 이러한 결함의 생성은 Si-H 결합의 파괴에 의해 발생할 수 있다는 것을 중수소 열처리 및 추가 수소 열처리 실험으로부터 발견하였다. OFF 전류 및 여러 가지 MOSFET의 전기적 특성의 변화는 관찰된 결함 전하(charge-trapping)의 생성과 직접적인 관련이 있다. 그러므로 실험 결과들로부터 게이트 산화막으로 터널링되는 전자나 정공에 의한 Si 및 O의 결합 파괴가 게이트 산화막 열화의 원인이 된다고 판단된다. 이러한 물리적 해석은 기존의 Anode-Hole Injection 모델과 Hydrogen-Released 모델의 내용을 모두 포함하게 된다.

• Molecules and Cells
• /
• 제37권4호
• /
• pp.322-329
• /
• 2014

N-acetylglucosamine kinase (GlcNAc kinase or NAGK; EC 2.7.1.59) is highly expressed and plays a critical role in the development of dendrites in brain neurons. In this study, the authors conducted structure-function analysis to verify the previously proposed 3D model structure of GlcNAc/ATP-bound NAGK. Three point NAGK mutants with different substrate binding capacities and reaction velocities were produced. Wild-type (WT) NAGK showed strong substrate preference for GlcNAc. Conversion of Cys143, which does not make direct hydrogen bonds with GlcNAc, to Ser (i.e., C143S) had the least affect on the enzymatic activity of NAGK. Conversion of Asn36, which plays a role in domain closure by making a hydrogen bond with GlcNAc, to Ala (i.e., N36A) mildly reduced NAGK enzyme activity. Conversion of Asp107, which makes hydrogen bonds with GlcNAc and would act as a proton acceptor during nucleophilic attack on the ${\gamma}$-phosphate of ATP, to Ala (i.e., D107A), caused a total loss in enzyme activity. The overexpression of EGFP-tagged WT or any of the mutant NAGKs in rat hippocampal neurons (DIV 5-9) increased dendritic architectural complexity. Finally, the overexpression of the small, but not of the large, domain of NAGK resulted in dendrite degeneration. Our data show the effect of structure on the functional aspects of NAGK, and in particular, that the small domain of NAGK, and not its NAGK kinase activity, plays a critical role in the upregulation of dendritogenesis.

• 한국진공학회:학술대회논문집
• /
• 한국진공학회 2009년도 제38회 동계학술대회 초록집
• /
• pp.4-5
• /
• 2010

The surface phonon is defined as a coherent vibrational excitation of surface atoms propagating along the surface. It is characterized by a phonon dispersion curves, which were extensively studied in 1990's using helium atom scattering and high-resolution electron-energy-loss spectroscopy (HREELS)[1].The understanding is mainly based on the theoretical framework of a classical bond model or cluster calculations. The recent sample preparation and first principles calculations open the naval way to deep insight for surface phonon problems. The surface phonon dispersion on the hydrogen-terminated Si(111)-($1{\times}1$) surface [H:Si(111)] is the typical system and already reported experimentally [2] and theoretically [3], although the understandingis incomplete. The sample contaminated by the oxygen atoms on the surface and the calculations were also classical. In this study, firstly, we have prepared an ultra-clean H:Si(111) surface [4] and measured the surface phonon dispersion curvesusing HREELS. Secondly, we have performed first-principles density functional calculations with the projector augmented wave functionals, as implemented in VASP, using generalized gradient approximations. We used aslab of six silicon layers and both top and bottom surfaces were terminated with hydrogen atoms. Finally, we have compared with the surface phonon dispersion of deuterium-terminatedSi(111)-($1{\times}1$) surface[5] and led to our conclusions. The Si-H stretching and the bending modes are observed at 258.5 and 78.2 meV, respectively. These energies are the same as the previously reported values [2], but the energy-loss peaks at the lower energy regions are dramatically shifted. Through this combination study, we have formulated the procedure of preparing ultra-clean H:Si(111)/D:Si(111), which was confirmed by HREELS vibrational analysis. The Si surface will be utilized for further nano-physics research as well as for the materials for nano-fubrication.

• Steel and Composite Structures
• /
• 제23권4호
• /
• pp.409-420
• /
• 2017

This paper theoretically studies the cyclic behavior of hybrid connections between steel coupling beams and concrete shear walls with embedded steel columns. Finite element models of connections with long and short embedded steel columns are built in ABAQUS and validated against the test results in the companion paper. Parametric studies are carried out using the validated FE model to determine the key influencing factors on the load-bearing capacity of connections. A close-form solution of the load-bearing capacity of connections is proposed by considering the contributions from the compressive strength of concrete at the interface between the embedded beam and concrete, shear yielding of column web in the tensile region, and shear capacity of column web and concrete in joint zone. The results show that the bond slip between embedded steel members and concrete should be considered which can be simulated by defining contact boundary conditions. It is found that the loadbearing capacity of connections strongly depends on the section height, flange width and web thickness of the embedded column. The accuracy of the proposed calculation method is validated against test results and also verified against FE results (with differences within 10%). It is recommended that embedded steel columns should be placed along the entire height of shear walls to facilitate construction and enhance the ductility. The thickness and section height of embedded columns should be increased to enhance the load-bearing capacity of connections. The stirrups in the joint zone should be strengthened and embedded columns with very small section height should be avoided.