• Bulletin of the Korean Chemical Society
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• v.19 no.10
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• pp.1047-1054
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• 1998

We present the results of molecular dynamics simulations for three different systems of bilayers of long-chain alkyl thiol [S(CH2)15CH3] molecules on an solid-solid interface using the extended collapsed atom model for the chain-molecule. It is found that there exist two possible transitions: a continuous transition characterized by a change in molecular interaction between sites of different chain molecules with increasing area per molecule and a sudden transition from an ordered lattice-like state to a liquid-like state due to the lack of interactions between sites of chain molecules on different surfaces with increasing distance between two solid surfaces. The third system displays a smooth change in probability distribution characterized by the increment of gauche structure in the near-tail part of the chain with increasing area per molecule. The analyses of energetic results and chain conformation results demonstrate the characteristic change of chain structure of each system.

• Molecules and Cells
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• v.41 no.12
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• pp.1000-1007
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• 2018

Mitochondria and endoplasmic reticulum (ER) are essential organelles in eukaryotic cells, which play key roles in various biological pathways. Mitochondria are responsible for ATP production, maintenance of $Ca^{2+}$ homeostasis and regulation of apoptosis, while ER is involved in protein folding, lipid metabolism as well as $Ca^{2+}$ homeostasis. These organelles have their own functions, but they also communicate via mitochondrial-associated ER membrane (MAM) to provide another level of regulations in energy production, lipid process, $Ca^{2+}$ buffering, and apoptosis. Hence, defects in MAM alter cell survival and death. Here, we review components forming the molecular junctions of MAM and how MAM regulates cellular functions. Furthermore, we discuss the effects of impaired ER-mitochondrial communication in various neurodegenerative diseases.

• Horticultural Science & Technology
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• v.29 no.5
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• pp.461-466
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• 2011

In genetic and molecular breeding studies of plants, researchers need to design various kinds of primers based on their research purposes. So far many kinds of web- or script-based non-commercial programs for primer design are available. Because most of them do not include user interface for multipurpose usage including gene structure prediction and direct target selection on sequences, it has been a laborious work to design primers targeting on the exon or intron regions of interesting genes. Here we report a primer designing graphic user interface program, Pickprimer, that includes gene structure prediction and primer design modules by combining source codes of the Spidey and Primer3 programs. This program provides simple graphic user interface to input sequences and design primers. Genomic sequence and mRNA or coding sequence of genes can be copy and pasted or input as fasta or text files. Based on alignment of the input sequences using the Spidey module, a putative gene structure is graphically visualized along with exon-intron sequences of color codes. Primer design can be easily performed by dragging mouse on the displayed sequences or input primer targeting position with desirable values of primers. The output of designed primers with detailed information is provided by the Primer3 module. PCR evaluation of 24 selected primer sets successfully amplified single amplicons from six Brassica rapa cultivars. The Pickprimer will be a convenient tool for genetic and molecular breeding studies of plants.

• Journal of the Computational Structural Engineering Institute of Korea
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• v.32 no.2
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• pp.103-108
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• 2019

Non-equilibrium molecular dynamics simulation on the thermal boundary resistance(TBR) of an aluminum(Al)/silicon(Si) interface was performed in the present study. The constant heat flux across the Si/Al interface was simulated by adding the kinetic energy in hot Si region and removing the same amount of the energy from the cold Al region. The TBR estimated from the sharp temperature drop at the interface was independent of heat flux and equal to $5.13{\pm}0.17K{\cdot}m^2/GW$ at 300K. The simulation result was experimentally confirmed by the time-domain thermoreflectance technique. A 90nm thick Al film was deposited on a Si(100) wafer using an e-beam evaporator and the TBR on the film/substrate interface was measured using the time-domain thermoreflectance technique based on a femtosecond laser system. A numerical solution of the transient heat conduction equation was obtained using the finite difference method to estimate the TBR value. Experimental results were compared to the prediction and discussions on the nanoscale thermal transport phenomena were made.

• Genomics & Informatics
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• v.3 no.3
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• pp.86-93
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• 2005

Human brain EST data provide important clues for our understanding of the molecular biology associated with the function of the normal brain and the molecular pathophysiology with brain disorders. To systematically and efficiently study the function and disorders of the human brain, 45,773 human brain ESTs were collected from 27 human brain cDNA libraries, which were constructed from normal brains and brain disorders such as brain tumors, Parkinson's disease (PO) and epilepsy. An analysis of 45,773 human brain ESTs using our EST analysis pipeline resulted in 38,396 high-quality ESTs and 35,906 ESTs, which were coalesced into 8,246 unique gene clusters, showing a significant similarity to known genes in the human RefSeq, human mRNAs and UniGene database. In addition, among 8,246 gene clusters, 4,287 genes ($52\%$) were found to contain full-length cONA clones. To facilitate the extraction of useful information in collected these human brain ESTs, we developed a user-friendly interface system, the Korea Brain Unigene Database (KBUD). The KBUD web interface allows access to our human brain data through three major search modes, the BioCarta pathway, keywords and BLAST searches. Each result when viewed in KBUD offers comprehensive information concerning the analyzed human brain ESTs provided by our data as well as data linked to various other publiC databases. The user-friendly developed KBUD, the first world-wide web interface for human brain EST data with ESTs of human brain disorders as well as normal brains, will be a helpful system for developing a better understanding of the underlying mechanisms of the normal brain well as brain disorders. The KBUD system is freely accessible at http://kugi.kribb.re.kr/KU/cgi -bin/brain. pI.

• Journal of Adhesion and Interface
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• v.13 no.3
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• pp.101-108
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• 2012

Narrowly dispersed poly(BMA-co-MMA) and PBMA latices (PSD : 1.002~1.008) were synthesized successfully by surfactant-free emulsion polymerization with 2,2' azobis(2-methyl-propionamidine) dihydrochloride (AIBA) and $K_2S_2O_8$ (KPS). The number average particle diameter and the number average molecule weight were found to be 160~494 nm and (1.25~7.55) ${\times}10^4$, respectively. The influences of BMA/MMA ratio, monomer and initiator concentrations, addition of DVB/EGDMA crosslink agent, and polymerization temperature on the polymerization rates and on the particle size and molecular weight were studied. The rate of polymerization increased with increasing MMA concentration in BMA/MMA weight ratio. The particle diameter as well as the polymer molecular weight could be controlled easily by controlling the BMA/MMA weight ratio, monomer concentration, AIBA and KPS concentration, and polymerization temperature.

• Journal of Adhesion and Interface
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• v.17 no.3
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• pp.89-95
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• 2016

An environmentally friendly water-based pressure sensitive adhesive (PSA) was designed in an attempt to replace the solvent-based adhesive for dry lamination used in flexible food packaging films. Instead of using a low molecular weight surfactant, which may have variable material properties, a high molecular weight dispersant was used for emulsification. A polymeric nano-dispersant (PND) was synthesized using solution polymerization, and it was used as a micelle seed in the surfactant, resulting in the synthesis of a core/shell grafted acrylic adhesive. The shell and core exhibited different $T_g$ values, so that the initial adhesion strength and holding power were complemented by the film's flexibility, which is required to provide good adhesion of thin films. Results showed that the PSA designed in this study using the PND instead of traditional low molecular weight surfactant had adhesive properties applicable to the flexible packaging with appropriate tack.

• Composites Research
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• v.31 no.6
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• pp.371-378
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• 2018

In this study, the thermoelastic properties of poly lactic acid (PLA) based nanocomposites are predicted by molecular dynamics (MD) simulation and a micromechanics model. The stereocomplex mixed with L-lactic acid (PLLA) and D-lactic acid (PDLA) is modeled as matrix phase and a single walled carbon nanotube is embedded as reinforcement. The glass transition temperature, elastic moduli and thermal expansion coefficients of pure matrix and nanocomposites unit cells are predicted though ensemble simulations according to the hydrolysis. In micromechanics model, the double inclusion (D-I) model with a perfect interface condition is adopted to predict the properties of nanocomposites at the same composition. It is found that the stereocomplex nanocomposites show prominent improvement in thermal stability and interfacial adsorption regardless of the hydrolysis. Moreover, it is confirmed from the comparison of MD simulation results with those from the D-I model that the interface between CNT and the stereocomplex matrix is slightly weak in nature.

• Current Photovoltaic Research
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• v.3 no.2
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• pp.61-64
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• 2015

In solar industry, numerous researchers reported about cold spray method among various electrode formation technic, but there are no known a bonding mechanism of metal powder. In this study, a cross-section of copper electrode formed by cold spray method was observed and heterogeneous phase between silicon substrate and copper electrode was analyzed using morphology observation technic. SEM and TEM analysis were performed to analyze a crystallinity and distribution shape of heterogeneous copper phase. Molecular dynamics simulation was performed to calculate glass transition temperature of copper metal. In the result, amorphous copper phase was observed near interface between silicon substrate and metal electrode. The results of the molecular dynamics simulation show that an amorphous copper phase could be formed at a temperature below the melting point of copper because cold spraying resulted in a lower glass transition temperature.

• The Transactions of the Korean Institute of Electrical Engineers
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• v.43 no.2
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• pp.303-311
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• 1994

Optimum conditions for the deposition of N-docosylquinolium-TCNQ ultrathin organic films using the Langmuir-Blodgett etchnique and the molecular orientation and alignment of the LB films were studied. The $\pi$-A isotherm of the N-docosylquinolium-TCNQ was measured at the air-water interface varying with the subphase temperature, subphase pH, compressing speed and amounts of solutions for spreading. The LB film was deposited under the surface pressure of 30mN.m and 45mN/m and other deposition conditions. The molecular orientation and alignment of the LB films were studied by the polarization absorption technique. The $\pi$-A isotherm showed that the stable N-docosylquinolium -TCNQ monolayer was formed on the water surface at the condition of 25$^{\circ}C$,pH 5.6, molecular density of 2.1${\times}$10S014T~2.6${\times}$10S014T/cmS02T. The LB film was deposited under the surface pressure of 45mN/m had better packing density, orientation and alignment than the film of 30mN/m.