• Journal of the Korean Magnetic Resonance Society
• /
• v.20 no.4
• /
• pp.129-137
• /
• 2016

Transmembrane(TM) proteins are closely related to transport, channel formation, signaling, cell to cell interaction, so they are the crucial target of modern medicinal drugs. In order to study the structure and function of these TM proteins, it is important to prepare reasonable amounts of proteins. However, their preparation is seriously difficult and time-consuming due to insufficient yields and low solubility of TM proteins. We tried to produce large amounts of Syndecan-4 containing TM domain(SDC4-TM) that is related to the wound healing and tumor. Also, mutated SDC4-TM was studied to investigate structural change by modification of dimerization motif. We performed the structure determination by the Polarity Index at Slanted Angle (PISA) wheel pattern analysis based on $^{15}N-^1H$ 2D SAMPI-4 solid-state NMR of SDC4-TM and computational modeling using Discovery Studio 2016.

• Bulletin of the Korean Chemical Society
• /
• v.7 no.6
• /
• pp.480-481
• /
• 1986

• Proceeding of EDISON Challenge
• /
• 2017.03a
• /
• pp.16-26
• /
• 2017

Auxin response factor (ARF) and Aux/IAA transcriptional repressor family proteins play a major role in auxin's signalling process. Using the GALAXY protein modelling programs, monomer, dimer and oligomer structures of Aux/IAA17 and ARF5 protein were predicted based on the known experimental structures. By analysing the proposed complex structures, key interacting residues on binding site could be determined, and further suggestions for experimental studies were made.

• Journal of the Korean Chemical Society
• /
• v.57 no.1
• /
• pp.99-103
• /
• 2013

The present communication deals with the Pharmacophore modeling, 3D QSAR and docking analysis on series of Pyrimidine derivatives as potential calcium channel blockers. The computational studies showed hydrogen bond donor, hydrogen bond acceptor, and hydrophobic group are important features for calcium channel blocking activity. These studies showed that Pyrimidine scaffold can be utilized for designing of novel calcium channels blockers for CVS disorders.

• Journal of Internet Computing and Services
• /
• v.21 no.3
• /
• pp.41-51
• /
• 2020

EDISON is a web-based platform that provides easy and convenient use of simulation software on high-performance computers. One of the most important roles of a computational science platform, such as EDISON, is to post-process and represent the simulation results data so that the user can easily understand the data. We interviewed EDISON users and collected requirements for post-processing and represent of simulation results, which included i) flexible data representation, ii) supporting various data representation components, and iii) flexible and easy development of view template. In previous studies, it was difficult to develop or contribute data representation components, and the view templates were not able to be shared or recycled. This causes a problem that makes it difficult to create ecosystems for the representation tool development of numerous simulation software. EDISON-VIEW is a framework for post-processing and representing simulation results produced from the EDISON platform. This paper proposes various methods used in the design and development of the EDISON-VIEW framework to solve the above requirements and problems. We have verified its usefulness by applying it to simulation software in various fields such as material, computational fluid dynamics, computational structural dynamics, and computational chemistry.

• Journal of Korean Society of Environmental Engineers
• /
• v.39 no.7
• /
• pp.426-439
• /
• 2017

This review summarizes advantage and limitation in infrared spectroscopy and computational chemistry to understand rhizospheric interaction among organic acids, oxyanions and metal oxides. Since organic acids and metal oxides determine dynamics of oxyanions in the soil environment, knowledge of fundamental mechanisms is a prerequisite for understanding the interactions at soil-water interface. Attenuated total reflectance-fourier transform infrared spectroscopy (ATR-FTIR) is a powerful tool to measure the interfacial reactions. However, the ATR-FTIR measurements are abstruse, because the optical characteristics for measurements are variable depending on the experimental setup. In addition, spectral overlapping is a primary obstacle to the analysis of the interfacial reaction; thus, it is essential to detect and to deconvolute bands for signal interpretation. In this review, we expained the fundamental principle for spectrum processing, and four band identification methods, such as derivative spectroscopy, two-dimension correlation spectroscopy, multivariate curve resolution, and computational chemistry with example of aqueous phosphate speciation. As a result, spectrum processing and computational chemistry improved interpretation and spectral deconvolution of overlapped spectra in relatively simple systems, but it was still unsatisfactory for the problems in more complexed system like nature. Nevertheless, we believed that our challenge would contribute practically to develop adequate analytical procedure, signal processing and protocols that could help to improve interpretation and to understand the interfacial interactions of oxyanions in natural systems.

• Bulletin of the Korean Chemical Society
• /
• v.26 no.6
• /
• pp.909-912
• /
• 2005

Calculations are presented for the structures of various conformers of the bare proline and proline –($H_2O$) cluster. The effects of hydrogen bonding with a water molecule on the relative stability of the low energy conformers of proline are examined. Microsolvation by a water molecule is predicted to affect the relative stability, structures and the infrared frequencies of the conformers to a large degree.

• Prospectives of Industrial Chemistry
• /
• v.22 no.4
• /
• pp.20-34
• /
• 2019

수소경제 시대의 도래와 함께 연료전지에 관한 연구가 크게 주목받고 있다. 그중 실험적으로 분석이 어려운 부분에 관하여 비용과 시간이 요구되는 실험적인 방법을 배제할 수 있는 모델링 기법인 전산유체역학(computational flow dynamics, CFD)이 큰 관심을 받고 있다. 연료전지의 연구에 주로 사용되는 전산유체역학에 관한 연구는 열분포, 유체의 흐름, 각종 반응물의 농도, 그리고 전기화학반응 등의 실험적인 분석이 현실적으로 불가능한 부분의 분석으로 통하여 실험을 줄이고도 많은 결과를 얻을 수 있는 연구가 활발하게 진행되고 있다. 본 기고문에서는 전산유체역학을 이용한 연료전지 내부에서 벌어지고 있는 각종 유체, 열, 전기화학반응 등에 관한 연구동향을 소개하고자 한다.

• Corrosion Science and Technology
• /
• v.16 no.1
• /
• pp.23-30
• /
• 2017

The inhibition effect of thioureido imidazoline inhibitor (TAI) for flow accelerated corrosion (FAC) at different locations for an X65 carbon steel elbow was studied by array electrode and computational fluid dynamics (CFD) simulations. The distribution of the inhibition efficiency measured by electrochemical impedance spectroscopy (EIS) is in good accordance with the distribution of the hydrodynamic parameters at the elbow. The inhibition efficiencies at the outer wall are higher than those at the inner wall meaning that the lower inhibition efficiency is associated with a higher flow velocity, shear stress, and turbulent kinetic energy at the inner wall of the elbow, as well as secondary flow at the elbow rather than the mass transport of inhibitor molecules. Compared to the static condition, the inhibition efficiency of TAI for FAC was relatively low. It is also due to a drastic turbulence flow and high wall shear stress during the FAC test, which prevents the adsorption of inhibitor and/or damages the adsorbed inhibitor film.

• Bulletin of the Korean Chemical Society
• /
• v.30 no.2
• /
• pp.423-428
• /
• 2009

The comparative study of three calix[4]heterocycles (calix[4]pyrrole, calix[4]furan, and calix[4]thiophene) has been theoretically performed by using high-level density functional theory (DFT) at the MPWB1K/6-311G$^{**}$//B3LYP/6- 311G$^{**}$ level. The effect of different hetero-atoms (nitrogen, oxygen, and sulfur) placed in the heterocycles on the conformational flexibility, thermodynamic stability order, cavity sizes, charge distributions, and binding propensities are examined. The thermodynamic stability differences between the conformers are found to be much greater in calix[4]pyrrole compared to those in calix[4]furan and calix[4]thiophene. Relatively larger NH group and higher dipole of a pyrrole ring in calix[4]pyrrole contribute to the higher energy barrier for the conformational conversions and relatively rigid potential energy surface compared to the case of calix[4]furan and calix[4]thiophene. The computational results herein provide theoretical understanding of the conformational flexibility and the thermodynamic nature which can be applied to understand the complexation behavior of the three calix[4]heterocycles.