• Asian Pacific Journal of Cancer Prevention
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• 제16권6호
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• pp.2561-2567
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• 2015

Pancreatic ductal adenocarcinoma (PDAC) is a leading cause of cancer death worldwide. Our study aimed to reveal molecular mechanisms. Microarray data of GSE15471 (including 39 matching pairs of pancreatic tumor tissues and patient-matched normal tissues) was downloaded from Gene Expression Omnibus (GEO) database. We identified differentially expressed genes (DEGs) in PDAC tissues compared with normal tissues by limma package in R language. Then GO and KEGG pathway enrichment analyses were conducted with online DAVID. In addition, principal component analysis was performed and a protein-protein interaction network was constructed to study relationships between the DEGs through database STRING. A total of 532 DEGs were identified in the 38 PDAC tissues compared with 33 normal tissues. The results of principal component analysis of the top 20 DEGs could differentiate the PDAC tissues from normal tissues directly. In the PPI network, 8 of the 20 DEGs were all key genes of the collagen family. Additionally, FN1 (fibronectin 1) was also a hub node in the network. The genes of the collagen family as well as FN1 were significantly enriched in complement and coagulation cascades, ECM-receptor interaction and focal adhesion pathways. Our results suggest that genes of collagen family and FN1 may play an important role in PDAC progression. Meanwhile, these DEGs and enriched pathways, such as complement and coagulation cascades, ECM-receptor interaction and focal adhesion may be important molecular mechanisms involved in the development and progression of PDAC.

• 한국생산제조학회지
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• 제24권4호
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• pp.421-427
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• 2015

In this paper, a description is given of finite element method (FEM) simulations of the elastic bending modulus of multi-layered graphene sheets that were carried out to investigate the mechanical behavior of graphene sheets with different gap thicknesses through molecular mechanics theory. The interaction forces between layers with various gap thicknesses were considered based on the van der Waals interaction. A finite element (FE) model of a multi-layered rectangular graphene sheet was proposed with beam elements representing bonded interactions and spring elements representing non-bonded interactions between layers and between diagonally adjacent atoms. As a result, the average elastic bending modulus was predicted to be 1.13 TPa in the armchair direction and 1.18 TPa in the zigzag direction. The simulation results from this work are comparable to both experimental tests and numerical studies from the literature.

• 한국진공학회:학술대회논문집
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• 한국진공학회 2011년도 제40회 동계학술대회 초록집
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• pp.24-25
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• 2011

Molecular self-assembly has several advantages over other nanofabrication methods. Molecular building blocks ensure ultrafine pattern precision, parallel structure formation allows for mass production and a variety of three-dimensional structures are available for fabricating complex structures. Nevertheless, the molecular interaction for self-assembly generally relies on weak forces such as van der Waals force, hydrogen bonding, or hydrophobic interaction. Due to the weak interaction, the structure formation is usually slow and the degree of ordering is low in a self-assembled structure. To promote self-assembly, directed assembly methods employing prepatterned substrates or external fields have been developed and gathered a great deal of technological attention as a next generation nanofabrication process. In this presentation a variety of directed assembly methods for soft nanomaterials including block copolymers, peptides and carbon nanomaterials will be introduced. Block copolymers are representative self-assembling materials extensively utilized in nanofabrication. In contrast to colloid assembly or anodized metal oxides, various shapes of nanostructures, including lines or interconnected networks, can be generated with a precise tunability over their shape and size. Applying prepatterned substrates$^{1,2}$ or introducing thickness modulation$^3$ to block copolymer thin films allowed for the control over the orientational and positional orderings of self-assembled structures. The nanofabrication processes for metals, semiconductors$^4$, carbon nanotubes$^{5,6}$, and graphene$^{6,7}$ templating block copolymer self-assembly will be presented.

• Bulletin of the Korean Chemical Society
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• 제30권5호
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• pp.1043-1046
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• 2009

Human protein tyrosine kinase-6 (PTK6) is a member of the non-receptor protein tyrosine kinase family and it is found in two-thirds of all breast tumors. Very recently, we proposed that the SH3 domain of PTK6 interacts with the linker region (Linker) between the SH2 and kinase domains, proving that the interaction between SH3 domain and Linker plays an important role in auto-inhibition mechanism. Residues from 1 to 191 corresponding region of SH3-SH2-Linker (SH32L) of PTK6 was cloned into the pET32a expression vector with Tobbaco etch virus (TEV) protease enzyme site by sequence homology and 3D structural model. The purified PTK6-SH32L was determined as a monomer conformation in solution. The amide proton resonances in the $^{15}N-^{1}H$ 2D-HSQC spectrum suggest that PTK6-SH32L possesses disordered structural region of the flexible/unstructured linker region. In addition, the backbone amide proton chemical shifts of the SH3 domain in the PTK6-SH32L differ from that of the independent domain, indicating that intra-molecular interaction between SH3 and Linker in the PTK6-SH32L is present.

• Bulletin of the Korean Chemical Society
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• 제4권5호
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• pp.223-227
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• 1983

A molecular dynamic computer experiment was performed on a system of 108 particles composed of a single polymer chain and solvent molecules. The state considered was in the immediate neighborhood of the triple point of the system. The polymer itself is an analog of a freely jointed chain. The Lennard-Jones potential was used to represent the interactions between all particles except for that between the chain elements forming a bond in the polymer chain, for which the interaction was expressed by a harmonic potential. The self-diffusion coefficient and velocity autocorrelation function (VACF) of a polymer were calculated at various chain lengths $N_p$, and various interaction strengths between solvent molecules and a polymer chain element. For self-diffusion coefficients D, the Einstein relation holds good; as chain length $N_p$ increases the D value decreases, and D also decreases as ${\varepsilon}_{cs}$ (the interaction parameter between the chain element and solvent molecules) increases. The relaxation time of velocity autocorrelation decreases as ${\varepsilon}_{cs}$ increases, and it is constant for various chain lengths. The diffusion coefficients in various conditions reveal that our systems are in a free draining limit as is well known from the behavior of low molecular weight polymers, this also agrees with the Kirkwood-Riesman theory.

• International Journal of Industrial Entomology and Biomaterials
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• 제11권2호
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• pp.119-124
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• 2005

To determine the level of heterosis, higher cocoon shell weight multivoltine congenic lines (Con. L) and bivoltine syngenic lines (Syn. L) of silkworm were used for crosses. First filial generations $(F_1s)$ expressed heterobeltiotic genetic interaction at significant magnitude (p < 0.01) for single cocoon shell weight (SCSW). The other linked characters viz., single cocoon weight (SCW) and yield by weight per 10, 000 larvae were also significantly higher (p < 0.01) than the better parental lines. All the hybrids showed significant improvement for these aforesaid characters over standard heterosis (Standard check). The reeling parameters viz., filament length, raw silk, neatness, cohesionstrokes etc, also showed improvement among the hybrids than check in congenial environment. Overall results suggested that the cross between congenic and syngenic lines provide better heterosis with good quality silk than conventional hybrids and may be used for commercial exploitation.

• The Plant Pathology Journal
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• 제30권4호
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• pp.425-431
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• 2014

Leaf scald caused by the infection of Rhynchosporium secalis, is a worldwide crop disease resulting in significant loss of barley yield. In this study, a systematic sequencing of expressed sequence tags (ESTs) was chosen to obtain a global picture of the assembly of genes involved in pathogenesis. To identify a large number of plant ESTs, which are induced at different time points, an amplified fragment length polymorphism (AFLP) display of complementary DNA (cDNA) was utilized. Transcriptional changes of 140 ESTs were observed, of which 19 have no previously described function. Functional annotation of the transcripts revealed a variety of infection-induced host genes encoding classical pathogenesis-related (PR) or genes that play a role in the signal transduction pathway. The expression analyses by a semi-quantitative reverse transcription polymerase chain reaction (RT-PCR) revealed that Rar1 and Rpg4 are defense inducible genes, and were consistent with the cDNA-AFLP data in their expression patterns. Hence, the here presented transcriptomic approach provides novel global catalogue of genes not currently represented in the EST databases.

• Bulletin of the Korean Chemical Society
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• 제26권8호
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• pp.1203-1208
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• 2005

A computational study based on molecular dynamics (MD) simulations was performed in order to explain the difference in aqueous solubilities of two flavonoid/$\beta$-cyclodextrin ($\beta$-CD) complexes, hesperetin/$\beta$-CD and naringenin/$\beta$-CD. The aqueous solubility of each flavonoid/$\beta$-CD complex could be characterized by complexwater interaction not by flavonoid-CD interaction. The radial distribution of water around each inclusion complex elucidated the difference of an experimentally observed solubility of each flavonoid/$\beta$-CD complex. The analyzed results suggested that a bulky hydrophobic moiety (-$OCH_3$) of B-ring of hesperetin nearby primary rim of $\beta$-CD was responsible for lower aqueous solubility of the hesperetin/$\beta$-CD complex.

• Bulletin of the Korean Chemical Society
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• 제32권12호
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• pp.4195-4198
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• 2011

Intramolecular ${\pi}-{\pi}$ and ${\sigma}-{\pi}$ interactions are omnipresent for numerous energetic and structural phenomena in nature, and the exact description of these nonbonding interactions plays an important role in the accurate prediction of the three-dimensional structures for numerous interesting molecular systems such as protein folding and polymer shaping. We have selected two prototype molecular systems for benchmarking calculations of intramolecular ${\pi}-{\pi}$ and ${\sigma}-{\pi}$ interactions. Accurately describing conformational energy of such systems requires highly elaborate but very expensive ab initio methods such as coupled cluster singles, doubles, and (triples) (CCSD(T)). Our calculations reveal a double hybrid density functional incorporating dispersion correction (B2PLYP-D) that agrees excellently with the CCSD(T) results, indicating that B2PLYP-D can serve as a practical method of choice.

• Bulletin of the Korean Chemical Society
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• 제4권2호
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• pp.87-91
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• 1983

Molecular dynamic method has been applied to a single polymer chain immersed in a solvent. The interactions for the pairs, of two solvent molecules (SS), of a chain element and a solvent molecules (CS), and of two non-neighbor chain elements (CC) are given by the Lennard-Jones potential, and the interaction between two bonded chain elements is given by a harmonic potential. We changed the CS interaction parameter ${\varepsilon}_{CS}$ to 0.5, 1.0 and 2.0 times of the SS interaction ${\varepsilon}_{SS}$. We calculated the pair correlation functions for the SS, CS, and CC pairs, end-to-end distance and radius of gyration with the varying ${\varepsilon}_{CS}$ parameters. The results showed that a phase separation occurs between the polymer and solvent in the 0.5 system where ${\varepsilon}_{CS}$ = 0.5 {\varepsilon}_{SS}$. The autocorrelation functions for end-to-end distance and radius of gyration were also calculated.