• Interaction and multiscale mechanics
• /
• 제4권3호
• /
• pp.219-237
• /
• 2011

Recent advances in scientific computing enable the full atomistic simulation of DNA molecules. However, there exists length and time scale limitations in molecular dynamics (MD) simulation for large DNA molecules. In this work, a two-level homogenization of DNA molecules is proposed. A wavelet projection method is first introduced to form a coarse-grained DNA molecule represented with superatoms. The coarsened MD model offers a simplified molecular structure for the continuum description of DNA molecules. The coarsened DNA molecular structure is then homogenized into a three-dimensional beam with embedded molecular properties. The methods to determine the elasticity constants in the continuum model are also presented. The proposed continuum model is adopted for the study of mechanical behavior of DNA loop.

• 한국콘크리트학회:학술대회논문집
• /
• 한국콘크리트학회 2006년도 춘계 학술발표회 논문집(II)
• /
• pp.77-80
• /
• 2006

Graft copolymerized polycarboxylate(PC)-type superplasticizers(PCs) which have carboxylic acid with $\pi$ bond among the molecular structure and polyethyleneglycol methyl ether methacrylate(PMEM) were synthesized by free radical reaction and investigated the chemical structure, polymerization condition, and physical and chemical properties. Also, the effects of PCs in the dispersion, adsorption and hydration of cement were evaluated. As the molecular weight of graft chain decreases, the adsorption amount on cement particles increased. It was advantageous for the flow to reduce molar ratio, the lower the side bone molecular weight, and increase the molar ratio, the larger the side bone molecular weight. The hydration reaction speed was highly delayed at day 1, due to increase in molar ratio and reduction in side bone molecular weight, but it was recovered in the days after.

• BMB Reports
• /
• 제35권6호
• /
• pp.590-594
• /
• 2002

To elucidate the effect of gamma-irradiation on the molecular properties of myoglobin, the secondary and tertiary structures, as well as the molecular weight size of the protein, were examined after irradiation at various irradiation doses. Gamma-irradiation of myoglobin solutions caused the disruption of the ordered structure of the protein molecules, as well as degradation, cross-linking, and aggregation of the polypeptide chains. A SDS-PAGE study indicated that irradiation caused initial fragmentation of the proteins and subsequent aggregation, due to cross-linking of the protein molecules. The effect of irradiation on the protein was more significant at lower protein concentrations. Ascorbic acid protected against the degradation and aggregation of proteins by scavenging oxygen radicals that are produced by irradiation. A circular dichroism study showed that an increase of the irradiation decreased the a-helical content of myoglobin with a concurrent increase of the aperiodic structure content. Fluorescence spectroscopy indicated that irradiation increased the emission intensity that was excited at 280 nm.

• Bulletin of the Korean Chemical Society
• /
• 제32권7호
• /
• pp.2433-2442
• /
• 2011

The three dimensional quantitative structure activity relationship (3D QSAR) models were developed using Comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA) and docking studies. The fit of Quinazolinone antifolates inside the active site of modeled bovine dihydrofolate reductase (DHFR) was assessed. Both ligand based (LB) and receptor based (RB) QSAR models were generated, these models showed good internal and external statistical reliability that is evident from the $q^2_{loo}$, $r^2_{ncv}$ and $r^2_{pred}$. The identified key features enabled us to design new Quinazolinone analogues as DHFR inhibitors. This study is a building bridge between docking studies of homology modeled bovine DHFR protein as well as ligand and target based 3D QSAR techniques of CoMFA and CoMSIA approaches.

• Preventive Nutrition and Food Science
• /
• 제7권2호
• /
• pp.184-187
• /
• 2002

Blood products from slaughterhouses that are not hygienically prepared for disposal or food consumption pose a human health hazard. Gamma irradiation is an effective method for sterilization of blood products, but may introduce changes in the molecular characteristics of proteins. This study evaluated the effects of irradiation on animal plasma proteins. Bovine and porcine blood was obtained from a slaughterhouse and the plasma proteins purified and lyophilized. The secondary structure and molecular weight distribution of the plasma protein solutions and powders were examined after ${\gamma}$-irradiation at 1, 5, 7 and 10 kGy. Gamma-irradiation affected the molecular properties of the protein solutions, but not the protein powders. Circular dichroism and sodium dodecyl sulfate-polyacrylamide gel electrophoresis studies showed that increased doses of ${\gamma}$-irradiation decrease the ordered structure of plasma proteins in solution, and cause initial fragmentation of the polypeptide chains and subsequent aggregation.

• 약학회지
• /
• 제54권1호
• /
• pp.62-66
• /
• 2010

Benzopyrene is known to be one of the most powerful carcinogens which can build intercalated motif between base pairs in damaged DNA. The dimension of benzopyrene itself is much bigger than any of the DNA bases and thus the question whether the lesion of some base pair by insertion of benzopyrene can happen with or without a dramatic distortion of the helical structure is a highly interesting theme. In this work we used a molecular mechanics simulation using AMBER program package to go into the conformational characteristics. The condition of the insertion process of the benzopyrene motif from minor groove of the starting structure between the base pairs in the internal area of double helix was investigated using the molecular dynamics simulation at elevated temperature.

• 대한방사성의약품학회지
• /
• 제2권1호
• /
• pp.3-8
• /
• 2016

Molecular imaging technologies have been used to provide a new pathway for therapies and diagnosis of human disease. Especially, imaging probes have been much development in the molecular imaging field. Combining imaging probes for positron emission tomography (PET) and magnetic resonance imaging (MRI) have suggested the potential of multiple methods in living body. This review discusses the cancer or lymph node-targeting probes that are suitable for PET/MRI based diagnosis.

• 한국과학교육학회지
• /
• 제21권3호
• /
• pp.497-505
• /
• 2001

본 연구에서는 고등학생 165명을 대상으로 학생들의 분자 구조에 대한 개념 이해도와 인지 변인들 사이의 관계를 조사하였다. 학생들이 두 학기 동안 '고등학교 화학 II 과목을 학습한 후, 분자 구조에 대한 개념, 공간 지각 능력, 논리적 사고력, 기억 용량, 학습 접근 방식 검사를 실시하였다. 연구 결과, 분자 구조 개념에 대한 학생들의 이해는 불완전하였으며, 몇 가지 오개념이 발견되었다. 개념 검사 점수는 모든 인지 변인 검사 점수들과 유의미한 상관이 있었다. 개념 이해에 대한 인지 변인들의 예언력을 조사하기 위해 중다 회귀 분석을 실시하였다. 유의미 학습 접근 방식이 가장 큰 예언력을 나타내었고, 논리적 사고력, 기계적 학습 접근 방식, 기억 용량의 순으로 예언력이 컸다. 그러나 공간 지각 능력은 예언력이 없었다.

• Applied Biological Chemistry
• /
• 제51권4호
• /
• pp.276-280
• /
• 2008

식품 allergen 저감화 수단으로 자외선 조사의 타당성을 검토하고 자외선조사가 식품 단백질의 분자적 성질에 미치는 영향을 조사하고자 ovalbumin 용액에 자외선을 조사한 후 단백질의 분자량 분포와 2차구조 및 3차구조의 변화를 조사하였다. SDS-PAGE와 Gel permeation chromatography 결과 ovalbumin은 자외선 조사에 의하여 단백질이 분해되고 조사시간이 증가할수록 펩티드가 중합하는 형태를 나타냈다. Circular dichroism 연구는 자외선 조사에 의하여 ${\alpha}$-helix 구조가 감소하고 조사시간이 증가할 경우 compact denatured ovalbumin의 구조를 나타내는 2차구조의 변화를 나타냈다. 자외선 조사된 ovalbumin의 형광스펙트럼은 조사시간이 증가할수록 단백질의 maximum emission intensity가 감소하는 3차구조의 변화를 나타냈다. 결과적으로 자외선 조사는 ovalbumin의 분자적 성질을 변화시키며 allergen의 항원성을 변화시키는 수단으로 이용가능성을 시사한다.

• 한국신재생에너지학회:학술대회논문집
• /
• 한국신재생에너지학회 2011년도 추계학술대회 초록집
• /
• pp.122.2-122.2
• /
• 2011

Sulfur hexafluoride ($SF_6$), one of the most potent greenhouse gases, is known as a hydrate former and has been studied at the high pressure up to 1.3 GPa with gas mixtures and with aqueous surfactant. Since we regard $SF_6$ as a potential promoter molecule that can stabilize hydrate structure more effectively compare to the other promoters, further investigation is required to verify the stabilizing ability of $SF_6$ in the hydrate structure. However, the insoluble nature of $SF_6$ in water or gases hinders fine scale analyses. This work discusses the data obtained by using molecular dynamics simulations of structure II (sII) clathrate hydrates containing $SF_6$ and $H_2$. The simulations were performed using the TIP4P/Ice model for water molecule and a previously reported $SF_6$ molecular model (optimized at the pure $SF_6$ single phase system (Olivet and Vega, 2007)), and a $H_2$ molecular model (adapted from the THF+$H_2$ hydrate system (Alavi et al., 2006)). The simulations are performed to observe the stability of $SF_6$ and $H_2$ in the sII clathrate hydrate system with varying temperature and pressure conditions and occupancies of $SF_6$ and $H_2$, which cannot be easily tuned experimentally. We observe that stability of H2 enclathrated in the hydrate structure more affected by the occupancy of $SF_6$ molecules and temperature than pressure, which ranges from 1 to 100 bar.