• EDISON SW 활용 경진대회 논문집
• /
• 제3회(2014년)
• /
• pp.347-358
• /
• 2014

본 논문에서는 양자 역학적 분자 동역학(Quantum Mechanical/Molecular Mechanical-Molecular Dynamics, QM/MM-MD)을 통해 수용액에 녹아 있는 Potassium Thiocyanate의 dynamics를 연구했다. Umbrella sampling technique을 활용하여 association/dissociation에 해당하는 Free energy surface를 구했다. 두 개의 Free energy minimum이 녹아 있는 두 이온의 center of mass 사이의 거리가 $4{\AA}$일 때와 $5{\sim}6{\AA}$ 부근일 때 나타났으며 $4{\AA}$일 때 더 안정 했다. 본 논문에서는 $4{\AA}$일 때를 Contact Ion Pair(CIP) $6{\AA}$일 때를 Dissociation Ion Pair(DlP)라고 칭했다. 이 minimum들이 무엇인 지를 밝혀 내기 위해 추가 연구를 수행하였다. Free energy 상에서 가장 안정 할 때(CIP) solute인 Potassium thiocyanate의 구조를 살펴 봤더니 Potassium ion은 Thiocyanate ion의 Sulfur보다 Nitrogen side를 선호하였다. 그 원인을 알아보기 위해 salvation shell의 구조를 Radial distribution function을 통해 살펴 봤더니 물 분자가 Nitrogen보다 Sulfur와 더 강한 상호작용을 하고 있었다. 그로 인해 Potassium ion이 Nitrogen을 선호한단 결과가 나온 것이다. 한편, 두 번째 minimum은 물 분자가 Potassium 이온과 Thiocyanate 이온 사이에 flexible하게 bridging을 하는 구조였다. 또한 단순 양자 계산을 통해서도 비슷한 구조를 얻을 수 있었다. 그러나 QM 계산은 0K에서 수행하는 것이기 때문에 엔트로피 효과가 없는 계산이지만 본 연구는 온도 300K로 실제 용매와 가깝게 수행함으로써 고정되어 있는 구조가 아니라 엔트로피와 엔탈피가 균형적으로 존재하는 실제 용액 속에서의 구조를 처음으로 보여주는 것이다.

• Macromolecular Research
• /
• 제12권4호
• /
• pp.342-351
• /
• 2004

Poly(ethylene glycol) (PEG1K) and sulfonated PEG (PEG1K-SO$_3$) methacrylate (MA) copolymers have been prepared and characterized. The structures of the synthesized copolymers were confirmed by $^1$H and $^{13}$ C NMR spectroscopy and elemental analysis. The bulk characteristics of the copolymers were evaluated by viscosity and thermal analysis. The surface properties of the copolymers were investigated using dynamic contact angle measurements and electron spectroscopy for chemical analysis. The hydrophilicity of the surfaces modified with PEG1KMA or PEG1K-SO$_3$MA increased, possibly as a result of the orientation of the hydrophilic PEG1KMA/PEG1K-SO$_3$MA chains into the water phase. Platelets adhered less to the surfaces of the copolymers than they did to a polyurethane control. In addition, adhesion of platelets to the copolymer surfaces decreased upon increasing the chain density of PEG1KMA and sulfonated PEG1KMA in the copolymers. Both bacterial adhesion and protein adsorption were significantly reduced on the copolymer surfaces and their levels differ depending on the kind of surface or media.

• Bulletin of the Korean Chemical Society
• /
• 제31권11호
• /
• pp.3195-3200
• /
• 2010

We have performed molecular dynamics simulations of atomistic models of $C_{60}$ molecules and DMPC bilayer membranes to study the static and dynamic effects of carbon nanoparticles on biological membranes. All four $C_{60}$-membrane systems were investigated representing dilute and concentrated solutions of $C_{60}$ residing either inside or outside the membrane. The concentrated $C_{60}$ molecules in water phase start forming an aggregated cluster. Due to its heavy mass, the cluster tends to adhere on the surface of the bilayer membrane, hindering both translational and rotational diffusion of individual $C_{60}$. On the other hand, once $C_{60}$ molecules accumulate inside the membrane, they are well dispersed in the central region of the bilayer membrane. Because of the homogeneous dispersion of $C_{60}$ inside the membrane, each leaflet is pushed away from the center, making the bilayer membrane thicker. This thickening of the membrane provides more room for both translational and rotational motions of $C_{60}$ inside the membrane compared to that in the water region. As a result, the dynamics of $C_{60}$ inside the membrane becomes faster with increasing its concentration.

• 한국전기전자재료학회:학술대회논문집
• /
• 한국전기전자재료학회 2003년도 춘계학술대회 논문집 센서 박막재료 반도체 세라믹
• /
• pp.103-106
• /
• 2003

It is well known that the state of existence of molecules on the surface of water changes during compression of the molecules. Electric methods, such as measurement of the surface potential or displacement current are also useful for investigating dynamic changes of molecular state on the water surface during compression. In this paper, We studied on the Bio thin film by Langmuir-Biodgett(LB) method. The Experiment method used displacement current, $\pi-A$ isotherm and BAM (Brewster Angle Microscopy). using the BAM, we can to the molecular orientation of monolayer on the water surface and directly see the morphology of the films on water subphase as well as that of the films.

• Journal of Preventive Medicine and Public Health
• /
• 제40권2호
• /
• pp.185-190
• /
• 2007

Objectives : Since the first human infection from avian influenza was reported in Hong Kong in 1997, many Asian countries have confirmed outbreaks of highly pathogenic H5N1 avian influenza viruses. In addition to Asian countries, the EU authorities also held an urgent meeting in February 2006 at which it was agreed that Europe could also become the next target for H5N1 avian influenza in the near future. In this paper, we provide the general and applicable information on the avian influenza in the bioinformatics field to assist future studies in preventive medicine. Methods : We introduced some up-to-date analytical tools in bioinformatics research, and discussed the current trends of avian influenza outbreaks. Among the bioinformatics methods, we focused our interests on two topics: pattern analysis using the secondary database of avian influenza, and structural analysis using the molecular dynamics simulations in vaccine design. Results : Use of the public genome databases available in the bioinformatics field enabled intensive analysis of the genetic patterns. Moreover, molecular dynamic simulations have also undergone remarkable development on the basis of the high performance supercomputing infrastructure these days. Conclusions : The bioinformatics techniques we introduced in this study may be useful in preventive medicine, especially in vaccine and drug discovery.

• Bulletin of the Korean Chemical Society
• /
• 제17권8호
• /
• pp.735-744
• /
• 1996

We present results of molecular dynamic (MD) simulations for the thermodynamic and structural properties of liquid n-alkanes, from n-butane to n-heptadecane, using three different models Ⅰ-Ⅲ. Two of the three classes of models are collapsed atomic models while the third class is an atomistically detailed model. Model Ⅰ is the original Ryckaert and Bellemans' collapsed atomic model [Discuss. Faraday Soc. 1978, 66, 95] and model Ⅱ is the expanded collapsed model which includes C-C bond stretching and C-C-C bond angle bending potentials in addition to Lennard-Jones and torsional potentials of model Ⅰ. In model Ⅲ all the carbon and hydrogen atoms in the monomeric units are represented explicitly for the alkane molecules. Excellent agreement of the results of our MD simulations of model Ⅰ for n-butane with those of Edberg et al.[J. Chem. Phys. 1986, 84, 6933], who used a different algorithm confirms the validity of our algorithms for MD simulations of model Ⅱ for 14 liquid n-alkanes and of models Ⅰ and Ⅲ for liquid n-butane, n-decane, and n-heptadecane. The thermodynamic and structural properties of models Ⅰ and Ⅱ are very similar to each other and the thermodynamic properties of model Ⅲ for the three n-alkanes are not much different from those of models Ⅰ and Ⅱ. However, the structural properties of model Ⅲ are very different from those of models Ⅰ and Ⅱ as observed by comparing the radial distribution functions, the average end-to-end distances and the root-mean-squared radii of gyrations.

• 폴리머
• /
• 제30권6호
• /
• pp.512-518
• /
• 2006

양친성 블록공중합체는 생분해성 고분자인 poly((R)-3-hydroxybutyrie acid), PHB와 친수성 고분자인 poly(ethylene glycol), PEG를 이용하여 제조되었다. 미생물에 의해 생산된 분자량이 수십만인 PHB는 약물전달용 재료로 적합하지 않으므로 산 촉매 가수분해를 통해 분자량이 $3000{\sim}30000$을 가지도록 조절되었다. 공중합체를 수용액에 넣으면, 고분자들은 자기 조립에 의해 친수성인 PEG가 소수성인 PHB를 감싸는 형태의 고분자 미셀을 형성한다. 형성된 고분자 미셀은 생분해성과 생체적합성을 가지면서 생체 내에서 낮은 독성과 환자 친화적인 특성을 가지므로 약물 전달체로의 이용이 가능하다. 양친성 블록 공중합체는 PHB에 PEG를 도입한 것으로 에스테르교환(transesterification) 반응을 통해 유도되었다. PEG는 친수성 블록의 형성과 반응성을 향상시키기 위해 말단의 작용기를 개질한 후 사용되었다. 양친성 블록 공중합체 형성에 대한 열적 특성과 화학적 구조 분석은 DSC, FTIR, $^1H-NMR$을 사용하여 알아보았다. 임계 미셀 농도(critical micelle concentration, CMC)는 고분자 미셀이 형성되는 시점으로 형광 분광기를 사용하여 분석한 결과 $5{\times}10^{-5}g/L$ 부근에서 측정되었다. 수용액 상의 고분자 미셀은 냉동 건조 후, 분말형태의 나노입자를 얻었다. 고분자 미셀의 크기는 dynamic light scattering으로 측정한 결과 약 130 nm 정도로 나타났다. 또한 atomic force microscopy 측정을 통해 크기가 약 130 nm 정도인 구형 입자를 확인하였다. 나노입자가 형성된 고분자 미셀은 소수성 약물을 담지하여 수동적 표적지향형 약물 전달용 수송체로 이용이 가능할 것이다.

• BMB Reports
• /
• 제40권2호
• /
• pp.261-269
• /
• 2007

The structure and dynamics of a 37-residue antimicrobial peptide gaegurin 4 (GGN4) isolated from the skin of the native Korean frog, Rana rugosa, was determined in SDS micelles by NMR spectroscopy. The solution structure of the peptide in SDS micelles was determined from 352 NOE-derived distance constraints and 22 backbone torsion angle constraints. Dynamic properties for the amide backbone were characterized by $^1H-^{15}N $heteronuclear NOE experiments. The structural study revealed two amphipathic helices spanning residues 2-10 and 16-32 and that the helices were connected by a flexible loop. An intraresidue disulfide bridge was formed between residues Cys31 and Cys37 near the C-terminus. The loop region (11-15) connecting the two helices are were slightly more flexible than these helices themselves. From the fact that since there is no contact NOEs between two helices, it is implied that the GGN4 peptide shows an independent motion of both helices which has an angle of about $ 60^{\circ}-120^{\circ}$ from each other.

• 대한기계학회논문집B
• /
• 제27권2호
• /
• pp.173-180
• /
• 2003

Effects of the electric conductivity of particles were studied for the aggregation process of charged particles with a Brownian dynamic simulation in the free molecular regime. A periodic boundary condition was used for the calculation of the aggregation process in each cell with 500 primary particles of 16 nm in diameter. We considered two extreme cases, a perfect conductor and a perfect nonconductor. The electrostatic force on a particle in the simulation cell was considered as a sum of electrostatic forces from other particles in the original cell and its replicate cells. We assumed that aggregates were only charged with pre-charged primary particles. The morphological shape of aggregates was described in terms of the fractal dimension. The fractal dimension for the uncharged aggregate was D$_{f}$= 1.761. However, the fractal dimension decreased from 1.694 to 1.360 for the case of the perfect conductor, and from 1.610 to 1.476 for the case of the perfect nonconductor, with the increase of the average number of charges on the primary particle from 0.2 to 0.3. These values were smaller than that of the centered charge case.e.

• BMB Reports
• /
• 제47권9호
• /
• pp.475-482
• /
• 2014

Ubiquitin (Ub) is a versatile signaling molecule that plays important roles in a variety of cellular processes. Cellular Ub pools, which are composed of free Ub and Ub conjugates, are in dynamic equilibrium inside cells. In particular, increasing evidence suggests that Ub homeostasis, or the maintenance of free Ub above certain threshold levels, is important for cellular function and survival under normal or stress conditions. Accurate determination of various Ub species, including levels of free Ub and specific Ub chain linkages, have become possible in biological specimens as a result of the introduction of the proteomic approach using mass spectrometry. This technology has facilitated research on dynamic properties of cellular Ub pools and has provided tools for in-depth investigation of Ub homeostasis. In this review, we have also discussed the consequences of the disruption of Ub pool dynamics and homeostasis via deletion of polyubiquitin genes or mutations of deubiquitinating enzymes. The common consequence was a reduced availability of free Ub and a significant impact on the function and viability of cells. These observations further indicate that the levels of free Ub are important determinants for cellular protection.