• Bulletin of the Korean Chemical Society
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• 제29권2호
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• pp.438-444
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• 2008

A self-assembled monolayer of 2,2'-bipyridine (22BPY) molecules on Au(111) underwent a structural phase transition when the polarity of a bias voltage was switched in scanning tunneling microscopy (STM) experiments. The nature of two bright spots representing each 22BPY molecule on Au(111) in the high-resolution STM images was identified by calculating the partial density plots for a monolayer of 22BPY molecules adsorbed on Au(111) using tight-binding electronic structure calculations. The stacking pattern of the chains of 22BPY molecules on Au(111) was explained by examining the intermolecular interactions between the 22BPY molecules based on first principles electronic structure calculations for a 22BPY dimer, (22BPY)2. The structural instability of the 22BPY molecule arrangement caused by a change in the bias voltage switch was investigated by estimating the adsorbate-surface interaction energy using a point-charge approximation for Au(111).

• Korean Chemical Engineering Research
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• 제56권5호
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• pp.607-624
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• 2018

SAFT 상태 방정식이 기초하는 TPT 이론과 통계역학적 원리를 개괄하고, 회합성 유체 혼합물의 기액 상평형을 예측하는 유용한 도구로 사용될 수 있음을 확인한다. PC-SAFT 상태 방정식의 이론적 구조를 상세히 검토하고, 비극성 혼합물, 극성혼합물, 회합성혼합물에단계적으로적용하는과정을통하여, 상태방정식의적용성과성능을평가한다. PC-SAFT 상태 방정식은 기존의 공학용 상태 방정식과는 대조적으로, 경험적인 이성분 상호작용 매개변수의 사용 없이 다양한 혼합물들의 비이상적 거동을 정확하게 예측할 수 있다. 이는 SAFT 이론이 분자들 사이의 다양한 상호작용을 효과적으로 반영하는 분자 수준의 엄밀한 이론 체계에 기초하기 때문이며, 다성분 혼합물의 복잡한 열역학적인 현상에 대한 응용에서 실질적 이점을 제공한다.

• 한국식물학회:학술대회논문집
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• 한국식물학회 1987년도 식물생명공학 심포지움 논문집 Proceedings of Symposia on Plant Biotechnology
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• pp.149-155
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• 1987

Growth and development of a higher plant, or any living organism for that matter, could be defined as an orderly expression of the genome in time and space in close interaction with the environment. During differentiation and development of a tissue or organ a group of genes must be selectively turned on or turned off mainly by trans-acting regulators. In this general concept of regulation of regulation of gene expression, a DNA molecule is recognized at a specific nucleotide sequence by DNA-binding factors. Molecular biology of the regulatory factors such as hormones, and their receptors, target DNA sequences and DNA-binding proteins are well advanced. What is not clearly understood is the molecular basis of the interactions between DNA and binding factors, expecially of the usages of the dyad symmetry of the target DNA sequences and the dimeric nature of the DNA-binding proteins. A unique 3-dimensional structure of DNA has been proposed that may play an important role in the orderly expression of the gene. A foldback intercoil (FBI) DNA configuration which was originally found by electron microscopy among mtDNA molecules from pearl millet has some unique features. The FBI configuration of DNA is believed to be formed when a flexible double helix folds back and interwines in the widened major grooves resulting in a four stranded, intercoil DNA whose thickness is the same as that of double stranded DNA. More recently, the FBI structure of DNA has been also induced in vitro by a novel enzyme which was purified from pearl millet mitochondria. It has been proposed that the FBI DNA could be utillized in intramolecular recombination which leads to inversion or deletion, and in intermolecular recombination which can lead to either site-specific recombination, genetic recombination via single strand invasion, or cross strand recombination. The structure and function of DNA in 3-dimensional aspect is emphasized for better understanding orderly expression of genes during growth and development.

• 폴리머
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• 제33권4호
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• pp.384-388
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• 2009

폴리아크릴로니트릴(PAN)과 셀룰로오스 아세테이트(CA) 블렌드/디메틸포름아미드(DMF) 용액의 유변학적 특성을 온도와 블렌드 조성비에 대하여 조사하였다. 모든 고분자 용액이 온도 변화에 따라 매우 특징적인 유변학적 거동을 보였다. 8 wt% 용액의 경우 $20{\sim}60^{\circ}C$ 온도범위에서 온도의 증가와 더불어 용액의 점도가 증가하고 손실탄젠트값이 감소하였다. $20^{\circ}C$에서는 용액의 물성이 블렌드의 조성에 영향을 받았으나 40 및 $60^{\circ}C$에서는 조성비가 용액 물성에 미치는 영향이 크게 감소하였다. 더 높은 온도에서의 더 긴 분자 이완시간으로부터 온도가 증가함에 따라 분자간력에 의한 물리적 구조 형성이 촉진된다는 것을 알 수 있었다. 이러한 유변학적 특성에 대한 원인은 묽은 용액의 특성으로부터 유추할 수 있었다. 고분자 용액의 고유점도가 온도가 증가함에 따라 감소하였다.

• Molecules and Cells
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• 제43권3호
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• pp.286-297
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• 2020

Mammalian patatin-like phospholipase domain containing proteins (PNPLAs) play critical roles in triglyceride hydrolysis, phospholipids metabolism, and lipid droplet (LD) homeostasis. PNPLA7 is a lysophosphatidylcholine hydrolase anchored on the endoplasmic reticulum which associates with LDs through its catalytic region (PNPLA7-C) in response to increased cyclic nucleotide levels. However, the interaction of PNPLA7 with LDs through its catalytic region is unknown. Herein, we demonstrate that PNPLA7-C localizes to the mature LDs ex vivo and also colocalizes with pre-existing LDs. Localization of PNPLA7-C with LDs induces LDs clustering via non-enzymatic intermolecular associations, while PNPLA7 alone does not induce LD clustering. Residues 742-1016 contains four putative transmembrane domains which act as a LD targeting motif and are required for the localization of PNPLA7-C to LDs. Furthermore, the N-terminal flanking region of the LD targeting motif, residues 681-741, contributes to the LD targeting, whereas the C-terminal flanking region (1169-1326) has an anti-LD targeting effect. Interestingly, the LD targeting motif does not exhibit lysophosphatidylcholine hydrolase activity even though it associates with LDs phospholipid membranes. These findings characterize the specific functional domains of PNPLA7 mediating subcellular positioning and interactions with LDs, as wells as providing critical insights into the structure of this evolutionarily conserved phospholipid-metabolizing enzyme family.

• 멤브레인
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• 제5권2호
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• pp.89-96
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• 1995

Azobenzene기를 가지는 인산형 양친매성 화합물의 기/액 계면에 있어서으 단분자막 거동이 $\pi-A$ 곡선 및 표면흡수스펙트라로 검토되었다. 분자간의 강한 수소결합력을 가지는 이 화합물들은 수면에 전개 후 즉시 결정화하여 단분자막 domain들을 형성한 회합체 흡수스펙트라를 나타내었다. 그러나 subphase의 조건(분자량이 큰 유가염의 첨가 및 pH의 상승)을 변화시킴에 의해 결정 domain 형성을 제어하는 것이 가능하였다. 한편, 금속이온 첨가는 인산령 양친매성 단분자막의 분재배향상태를 변화시켰다. 금속이온의 전하가 높을수록 ($1\leq2$ < 3 < 4 가), azobenzene기를 가지는 양친매성 화합물의 분자상태가 tilt된 배향성에 기인하는 장파장으로 이동한 흡수극대를 나타내었다. 이것은 서로 다른 전하를 가진 금속이온을 흡착시킴에 의해 단분자막의 분자배향성을 변화시켜, 단분자막의 집합상태 제어 가능성을 시사한다.

• Genomics & Informatics
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• 제14권2호
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• pp.53-61
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• 2016

Toxoplasma gondii is an intracellular Apicomplexan parasite and a causative agent of toxoplasmosis in human. It causes encephalitis, uveitis, chorioretinitis, and congenital infection. T. gondii invades the host cell by forming a moving junction (MJ) complex. This complex formation is initiated by intermolecular interactions between the two secretory parasitic proteins-namely, apical membrane antigen 1 (AMA1) and rhoptry neck protein 2 (RON2) and is critically essential for the host invasion process. By this study, we propose two potential leads, NSC95522 and NSC179676 that can efficiently target the AMA1 hydrophobic cleft, which is a hotspot for targeting MJ complex formation. The proposed leads are the result of an exhaustive conformational search-based virtual screen with multilevel precision scoring of the docking affinities. These two compounds surpassed all the precision levels of docking and also the stringent post docking and cumulative molecular dynamics evaluations. Moreover, the backbone flexibility of hotspot residues in the hydrophobic cleft, which has been previously reported to be essential for accommodative binding of RON2 to AMA1, was also highly perturbed by these compounds. Furthermore, binding free energy calculations of these two compounds also revealed a significant affinity to AMA1. Machine learning approaches also predicted these two compounds to possess more relevant activities. Hence, these two leads, NSC95522 and NSC179676, may prove to be potential inhibitors targeting AMA1-RON2 complex formation towards combating toxoplasmosis.

• 한국진공학회:학술대회논문집
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• 한국진공학회 2009년도 제38회 동계학술대회 초록집
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• pp.358-358
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• 2010

Ion beam bombardment at low energy forms nanosize patterns such as ripples, dots or wrinkles on the surface of polymers in ambient temperature and pressure. It has been known that the ion beam can alter the polymer surface that induces skins stiffer or the density higher by higher compressive stress or strain energies associated with chain scissions and crosslinks of the polymer. Atomic scale structure evolution in polymers is essential to understand a stress generation mechanism during the ion beam bombardment, which governs the nanoscale surface structure evolution. In this work, Molecular Dynamics (MD) simulations are employed to characterize the phenomenon occurred in bombardment between the ion beam and polymers that forms nanosize patterns. We investigate the structure evolution of Low Density Polyethylene (LDPE) at 300 K as the polymer is bombarded with Argon ions having various kinetic energies ranging from 100 eV to 1 KeV with 50 eV intervals having the fluence of $1.45\;{\times}\;1014 #/cm2$. These simulations use the Reactive Force Field (ReaxFF), which can mimic chemical covalent bonds and includes van der Waals potentials for describing the intermolecular interactions. The results show the details of the structural evolution of LDPE by the low energy Ar ion bombardment. Analyses through kinetic and potential energy, number of crosslinks and chain scissions, level of local densification and motions of atoms support that the residual strain energies on the surface is strongly associated with the number of crosslinks or scissored chains. Also, we could find an optimal Ar ion beam energy to make crosslinks well.

• Steel and Composite Structures
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• 제34권2호
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• pp.261-277
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• 2020

The main objective of this research paper is to consider vibration analysis of vacancy defected graphene sheet as a nonisotropic structure via molecular dynamic and continuum approaches. The influence of structural defects on the vibration of graphene sheets is considered by applying the mechanical properties of defected graphene sheets. Molecular dynamic simulations have been performed to estimate the mechanical properties of graphene as a nonisotropic structure with single- and double- vacancy defects using open source well-known software i.e., large-scale atomic/molecular massively parallel simulator (LAMMPS). The interactions between the carbon atoms are modelled using Adaptive Intermolecular Reactive Empirical Bond Order (AIREBO) potential. An isogeometric analysis (IGA) based upon non-uniform rational B-spline (NURBS) is employed for approximation of single-layered graphene sheets deflection field and the governing equations are derived using nonlocal elasticity theory. The dependence of small-scale effects, chirality and different defect types on vibrational characteristic of graphene sheets is investigated in this comprehensive research work. In addition, numerical results are validated and compared with those achieved using other analysis, where an excellent agreement is found. The interesting results indicate that increasing the number of missing atoms can lead to decrease the natural frequencies of graphene sheets. It is seen that the degree of the detrimental effects differ with defect type. The Young's and shear modulus of the graphene with SV defects are much smaller than graphene with DV defects. It is also observed that Single Vacancy (SV) clusters cause more reduction in the natural frequencies of SLGS than Double Vacancy (DV) clusters. The effectiveness and the accuracy of the present IGA approach have been demonstrated and it is shown that the IGA is efficient, robust and accurate in terms of nanoplate problems.

• The Korean Journal of Pain
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• 제34권3호
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• pp.262-270
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• 2021

Background: Transient receptor potential vanilloid 1 (TRPV1) is a non-selective cation channel implicated in pain sensation in response to heat, protons, and capsaicin (CAPS). It is well established that TRPV1 is involved in mechanical allodynia. This study investigates the effect of Ononis spinosa (Fabaceae) in CAPS-induced mechanical allodynia and its mechanism of action. Methods: Mechanical allodynia was induced by the intraplantar (ipl) injection of 40 ㎍ CAPS into the left hind paw of male Wistar rats. Animals received an ipl injection of 100 ㎍ O. spinosa methanolic leaf extract or 2.5% diclofenac sodium 20 minutes before CAPS injection. Paw withdrawal threshold (PWT) was measured using von Frey filament 30, 90, and 150 minutes after CAPS injection. A molecular docking tool, AutoDock 4.2, was used to study the binding energies and intermolecular interactions between O. spinosa constituents and TRPV1 receptor. Results: The ipsilateral ipl injection of O. spinosa before CAPS injection increased PWT in rats at all time points. O. spinosa decreased mechanical allodynia by 5.35-fold compared to a 3.59-fold decrease produced by diclofenac sodium. The ipsilateral pretreatment with TRPV1 antagonist (300 ㎍ 4-[3-Chloro-2-pyridinyl]-N-[4-[1,1-dimethylethyl] phenyl]-1-piperazinecarboxamide [BCTC]) as well as the β2-adrenoreceptor antagonist (150 ㎍ butoxamine) attenuated the action of O. spinosa. Depending on molecular docking results, the activity of the extract could be attributed to the bindings of campesterol, stigmasterol, and ononin compounds to TRPV1. Conclusions: O. spinosa alleviated CAPS-induced mechanical allodynia through 2 mechanisms: the direct modulation of TRPV1 and the involvement of β2 adrenoreceptor signaling.