• Bulletin of the Korean Chemical Society
• /
• v.32 no.7
• /
• pp.2237-2242
• /
• 2011

Anomalous scaling behaviors such as significantly large growth exponent (${\beta}$) and small reciprocal of dynamic exponent (1/z) values for many molecular crystalline thin films have been reported. In this study, the variation of scaling exponent values and consequent growth behaviors of molecular thin films were more quantitatively analysed using a (1+1)-dimensional surface lateral diffusion model. From these simulations, influence of step edge barriers and grain boundaries of molecular thin films on the various scaling exponent values were elucidated. The simulation results for the scaling exponents were also well consistent with the experimental data for previously reported molecular thin film systems.

• Bulletin of the Korean Chemical Society
• /
• v.20 no.11
• /
• pp.1323-1328
• /
• 1999

Interdiffusion between two partially miscible polymers of similar chemical structures with different molecular weights is characterized theoretically by using the reptation model for the interdiffusion. This model provides more reliable results than the early Rouse model for same molecular weights, compared with the experiments. Furthermore, by introducing the molecular weight ratio R into the reptation model, we can see the dynamic effect of molecular weight on the diffusion behaviors of the asymmetric system. Near the critical point the diffusion behaviors of asymmetric binary polymer mixtures are well characterized by the interfacial width W(t), the mass transport M(t) for the different values of the Flory Χ parameter and different molecular weight ratios ofpolymers of the diffusion couple. These two quantities and composition profiles by this model give betteragreement with experiments.

• Proceedings of the Korean Information Science Society Conference
• /
• 1998.10c
• /
• pp.51-53
• /
• 1998

3개 이상의 DNA 혹은 단백질의 염기서열을 정렬하는 복수 염기서열 정렬(multiple sequence alignment)방법은 염기서열들 사이의 진화관계, gene regulation, 단백질의 구조와 기능에 관한 연구에 필수적인 도구이다. 복수 염기서열 정렬문제는 NP-complete 문제군에 속하며, 이 문제를 해결하기 위하여 가장 유용하게 사용되는 알고리즘으로는 dynamic programming이 있다. Dynamic programming은 주어진 입력 염기서열 군들에 대한 최적의 정렬을 생산할 수 있다. 그러나 dynamic programming의 단점은 오랜 실행시간이 요구되며, 때로는 dynamic programming의 속성 때문에 이 알고리즘을 사용하여도 주어진 입력 염기서열 군들에 대한 최적의 정렬을 얻어내지 못하는 경우가 있다. 본 연구에서는 이러한 dynamic programming의 문제를 해결하기 위하여 genetic algorithm을 복수 염기서열 정렬문제에 적용하였다. 본 논문에서는 genetic algorithm의 design과 적용방법을 기술하였다. 본 연구에서 제안된 genetic algorithm을 사용하여 dynamic programming의 단점이었던 오랜 실행시간을 줄일 수 있었으며, dynamic programming이 제공하지 못하는 최적의 염기서열 정렬을 제공할 수 있었다.

• Journal of Radiopharmaceuticals and Molecular Probes
• /
• v.1 no.2
• /
• pp.123-129
• /
• 2015

$^{64}Cu$-labeled diacetyl-bis($N^4$-methylthiosemicarbazone) is a promising agent for internal radiation therapy and imaging of hypoxic tissues. In the study, we confirmed hypoxia regions in VX2 tumor implanted rabbits with injection $^{64}Cu$-ATSM and $^{18}F$-FDG using positron emission tomography (PET)/computed tomography (CT). PET images with $^{18}F$-FDG and $^{64}Cu$-ATSM were obtained for 40 min by dynamic scan and additional delayed PET images of $^{64}Cu$-ATSM the acquired up to 48 hours. Correlation between intratumoral $O_2$ level and $^{64}Cu$-ATSM PET image was analyzed. $^{64}Cu$-ATSM and $^{18}F$-FDG were intravenously co-injected and the tumor was dissected and cut into slices for a dual-tracer autoradiographic analysis. In the PET imaging, $^{64}Cu$-ATSM in VX2 tumors displayed a specific uptake in hypoxic region for48 h. The uptake pattern of $^{64}Cu$-ATSM in VX2 tumor at 24 and 48 h did not match to the $^{18}F$-FDG. Through ROI analysis, in the early phase (dynamic scan), $^{18}F$-FDG has positive correlation with $^{64}Cu$-ATSM but late phase (24 and 48 h) of the $^{64}Cu$-ATSM showed negative correlation with $^{18}F$-FDG. High uptake of $^{64}Cu$-ATSM in hypoxic region was responded with significant decrease of oxygen pressure, which confirmed by $^{64}Cu$-ATSM PET imaging and autoradiographic analysis. In conclusion, $^{64}Cu$-ATSM can utilize for specific targeting of hypoxic region in tumor, and discrimination between necrotic- and viable hypoxic tissue.

• Proceedings of the KSME Conference
• /
• 2007.05a
• /
• pp.337-342
• /
• 2007

In this study, molecular dynamics simulation of nano imprint lithography in which patterned stamp is pressed onto amorphous polyethylene(PE) surface are performed to study the behaviour of polymer. Force fields including bond, angle, torsion, and Lennard Jones potential are used to describe the inter-molecular and intra-molecular force of PE molecules and stamp, substrate. Periodic boundary condition is used in horizontal direction and canonical NVT ensemble is used to control the system temperature. As the simulation results, the behaviour of polymer is investigated during the imprinting process. The mechanism of polymer deformation is studied by means of inspecting the surface shape, volume, density, atom distribution. Deformation of the polymer resist was found for various of the stamp geometry and the alignment state of the polymer molecules.

• KSII Transactions on Internet and Information Systems (TIIS)
• /
• v.10 no.10
• /
• pp.5035-5048
• /
• 2016

Nano scale networks are futuristic networks deemed as enablers for the Internet of Nano Things, Body area nano networks, target tracking, anomaly/ abnormality detection at molecular level and neuronal therapy / drug delivery applications. Molecular communication is considered the most compatible communication technology for nano devices. However, connectivity in such networks is very low due to inter-symbol interference (ISI). Few research papers have addressed the issue of ISI mitigation in molecular communication. However, many of these methods are not adaptive to dynamic environmental conditions. This paper presents an enhancement over original Memory-1 ISI cancellation scheme using maximum likelihood estimation of a channel parameter (λ) to make it adaptable to variable channel conditions. Results of the Monte Carlo simulation show that, the connectivity (P_conn) improves by 28% for given simulation parameters and environmental conditions by using enhanced Memory-1 cancellation method. Moreover, this ISI mitigation method allows reduction in symbol time (Ts) up to 50 seconds i.e. an improvement of 75% is achieved.

• Advances in nano research
• /
• v.15 no.2
• /
• pp.105-111
• /
• 2023

Integrin αvβ3 is one of the receptors expressed in cancer cells. RGD peptides have the potential to target integrin αvβ3 (receptor), which can increase drug delivery efficiency. In this study, 55 different RGD dimer motifs were investigated. At first, the binding energy between RGD peptides and the receptor was calculated using molecular docking. Then, three RGD peptides with the strongest binding energy with the receptor were selected, and their dynamic adsorption on the receptor was simulated by molecular dynamics (MD). The obtained results showed that a sequence that has RGD at the beginning and end with tryptophan (TRP) has strong Lennard-Jones (LJ) and electrostatic interactions with Integrin αvβ3 and has changed the conformation of receptor significantly, which analyzed by root mean square deviation (RMSD) and radius of gyration.

• Animal cells and systems
• /
• v.7 no.3
• /
• pp.207-211
• /
• 2003

Caveolin-1 is a principal protein in the plasma membrane microdomains called caveolae. Caveolae play an important role in the transcytosis and pinocytosis. Therefore, caveolin-1 is most likely to work for the membrane dynamic events. In addition, caveolin-1 interacts with various signaling molecules. Although caveolin-1 possesses a variety of physiological functions, its structural properties were little construed. Here we analyzed the structural dynamics of the N-terminal caveolin-1 (residues 1-101), in order to better understand the structural properties in terms of its versatile functionality. We first analyzed its oligomeric form using GST-fused N-terminal domain, revealing that it equilibrates between a dimer and monomers in av concentration-dependent manner. The N-terminal domain of caveolin-1 was previously found to form a heptamer, so that our data suggest the dimeric form as an intermediate structure for the heptamer formation. Then, we obtained the folding profile, which indicated that $\DeltaG_{H2O}\;is\;about\;0.5\;\pm0.03$ kcal/mol. The stability of N-terminal domain is relatively low, indicating that N-terminal domain may not be crystalline. Conclusively, the dynamic and flexible structure of N-terminal domain appears more favorable to maintain the versatile functions of caveolin-1.

• Bulletin of the Korean Chemical Society
• /
• v.25 no.12
• /
• pp.1845-1849
• /
• 2004

Apolipoprotein B-100 (Apo-B100) is a major protein component for low density lipoproteins (LDL). A number of mimetic peptides of Apo-B100 were screened from the phase-displayed random peptide library by utilizing monoclonal antibody (B9). Mimetic peptide for B9 epitope against apo B-100 was CRNVPPIFNDVYWIAF (pB1). From the BLAST search, the mimetic peptide pB1 had 40% homology with apo B-100. As a result of the structural determination of this mimotope using homo/hetero nuclear 2D-NMR techniques and NMR-based distance geometry (DG)/molecular dynamic (MD) computations, DG structure had low penalty value of 0.3-0.6 ${\AA}^2$ and the total RMSD was 0.5-1.5 ${\AA}. Moreover, pB1 structure included a weak $3_{10}$-helix from $Ile^7$,/TEX> to $Trp^{13}$.

• Korean Journal of Metals and Materials
• /
• v.47 no.1
• /
• pp.32-37
• /
• 2009

Molecular dynamic simulations on the structural evolution of the Si(001) vicinal surfaces, which are tilted with respect to [100] and [110] directions were performed by using the empirical Tersoff potential. Tersoff potential was implemented at LAMMPS code and confirmed to describe the properties of Si. When the steps are generated along [100] direction, symmetric dimer rows formed with respect to the step edges. On the other hand, when the steps are generated along [110] direction, alternating dimer rows form with respect to the step edges. The configurational differences between the two vicinal surfaces were discussed in terms of the surface diffusion and the possibility of preventing step bunching for the (001) vicinal surface tilted along [100] direction was suggested.