• KSII Transactions on Internet and Information Systems (TIIS)
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• v.15 no.8
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• pp.2923-2943
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• 2021

The double helix structure of DNA makes it diverse, stable and can store information with high density, and these characteristics are consistent with the requirements of molecular communication for transport carriers. In this paper, a specific structure of molecular communication system based on DNA length coding is proposed. Transmitter (Tx) adopts the multi-layer golden foil design to control the release of DNA molecules of different lengths accurately, and receiver (Rx) adopts an effective and sensitive design of nanopore, and the biological information can be converted to the electric signal at Rx. The effect of some key factors, e.g., the length of time slot, transmission distance, the number of releasing molecules, the priori probability, on channel capacity is demonstrated exhaustively. Moreover, we also compare the transmission capacity of DNA-based molecular communication (DNA-MC) system and concentration-based molecular communication (MC) system under the same parameter setting, and the peak value of capacity of DNA-MC system can achieve 0.08 bps, while the capacity of MC system remains 0.025 bps. The simulation results show that DNA-MC system has obvious advantages over MC system in saving molecular resources and improving transmission stability.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.56 no.5
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• pp.708-715
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• 2023

Hybridization is a major production method used to combine beneficial traits from two different species to obtain a potentially dominant trait. In China, Takifugu obscurus and T. rubripes were artificially crossed, and the resulting hybrids had an average body weight 38.06-8.93% higher than that of the parental species, which enabled the hybrids to be grown in freshwater. This study aimed to provide the basic data necessary for the classification of T. obscurus♀×T. rubripes♂ hybrids in terms of economic value and market potential. Morphological comparing the morphology of hybrids and parental species, we discovered that the hybrids had intermediate traits of the parental species. In morphometrics, the hybrid index (HI) value of head length against standard length was close to the trait of T. rubripes, and the HI values of preanal length and predorsal length were close to those of T. obscurus; however, the HI values of nasal length, snout length, length of anal fin, length of pectoral fin, caudal peduncle depth and caudal peduncle length were found to be unique characteristics of the hybrids. Regarding molecular analysis, a 99.8% nucleotide sequence similarity was found between the hybrid and T. obscurus.

• Journal of the Korean Society of Clothing and Textiles
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• v.24 no.7
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• pp.1065-1072
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• 2000

The molecular areas and the interfacial tension behavior of ten nonionic surfactants, i.e., Span 20 and Tween 20, 40, 60. 80, 21, 61, 81, 65, & 85 are tested to assay their effects on the wetting and liquid retention properties of hydrophilic and hydrophobic fibrous materials. The molecular areas at water/air interface are derived from Gibbs’adsorption equations. The following conclusions are drawn from the results: 1) Span 20 is efficient in lowering the interfacial tension and effective in adsorption at the water/air interface, resulting in the low interfacial tension at critical micelle concentration (${\gamma}$$_{CMC}$) and a small molecular area($\omega$), 2) when the hydrophiles of the surfactants are constant, $\omega$’s increase as hydrophobe carbon numbers of the surfactants increase, 3) when the hydrophobes are constant, ${\gamma}$$_{CMC}$’s and $\omega$’s increase as the hydrophile ethylene oxide units increase, indicating effectiveness and efficiency is parallel in this case, 4) the ethylene oxide unit length as a hydrophile has greater influence on u than the hydrophobe chain length.han the hydrophobe chain length.gth.

• Molecules and Cells
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• v.21 no.1
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• pp.135-140
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• 2006

Cytoplasmic male sterility (CMS) in plants, which is due to failure to produce functional pollen, is a maternally inherited trait. Specific nuclear genes that suppress CMS, termed fertility restorer (Rf) genes, have been identified in several plants. In this study, Rfl-inked molecular markers in pepper (Capsicum annuum L.) were detected by bulked segregant analysis of eight amplified fragment length polymorphisms (AFLPs). Only AFRF8 was successfully converted to a cleaved amplified polymorphic sequence (CAPS) marker. This was named AFRF8CAPS and genotype determination using it agreed with that obtained with the original AFRF8. A linkage map with a total size of 54.1 cM was constructed with AFRF8CAPS and the seven AFLP markers using the Kosambi function. The AFRF8CAPS marker was shown to be closest to Rf with a genetic distance of 1.8 cM. These markers will be useful for fast and reliable detection of restorer lines during $F_1$ hybrid seed production and breeding programs in pepper.

• Proceedings of the Computational Structural Engineering Institute Conference
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• 2007.04a
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• pp.421-426
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• 2007

A parametric study to investigate the effects of composition variables on the glass transition and mechanical properties of CNT-based nanocomposites was performed using molecular dynamics simulations. In this study, matrix chain length and CNT length were chosen as the candidate characteristic parameters. In order to understand the effect of both parameters in detail, three sample sets having different chain lengths with the same CNT configuration and two sample sets having different CNT lengths with same chain length were prepared. Other parameters such as volume fraction and density were fixed to enable rigorous comparisons. Amorphous polyethylene is used as matrix polymer and (10,0) zigzag CNT is embedded into the matrix to reinforce polymer matrix. As a result, longer polymer chain length of matrix solely increased glass transition temperature but no reinforcing enhancement was observed. CNT length showed similar increase with little enhancement of elastic modulus. In addition to this, nanocomposites showed temperature-dependent elastic modulus jump passing thorough the glass transition region agrees well with experimental results.

• Asian-Australasian Journal of Animal Sciences
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• v.17 no.7
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• pp.897-902
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• 2004

PSMC5 subunit, which belongs to the 26S proteasomal subunit family, plays an important role in the antigen presentation mediated by MHC class I molecular. Full-length cDNA of porcine PSMC5 was isolated using the in silico cloning and rapid amplification of cDNA ends (RACE). Amino acid was deduced and the primary structure was analyzed. Results revealed that the porcine PSMC5 gene shares the high degree of sequence similarity with its mammalian counterparts at both the nucleotide level and the amino acid level. The RT-PCR was performed to detect the porcine PSMC5 expression pattern in seven tissues and the result showed that high express level was observed in spleen, lung, marrow and liver while the low express level was in muscle. The full-length genomic DNA sequence of porcine PSMC5 gene was amplified by PCR and the genomic structure revealed that this gene was comprised by 12 exons and 11 introns. Best alignment of the cDNA and genomic exon DNA sequence presents 4 mismatches and this information potentially bears further study in gene polymorphisms.

• Journal of Microbiology and Biotechnology
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• v.17 no.7
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• pp.1098-1105
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• 2007

Quantum mechanical and molecular dynamics simulation analysis has been performed on the model system for CALB (Candida antarctica lipase B) with esters to study the reaction mechanism and conformational preference of catalytic hydrolysis and the esterification reaction. Using quantum mechanical analysis, the ping-pong bi-bi mechanism was applied and energies and 3-dimensional binding configurations of the whole reaction pathways were calculated. Further molecular dynamics simulation analysis was performed on the basis of the transition state obtained from quantum mechanical study to observe the effect of structures of the substrates. Calculation results using substrates of different chain length and chiral configurations were compared for conformational preference. The calculated results showed very small influence on chain length, whereas chiral conformation showed big differences. Calculated results from molecular modeling studies have been compared qualitatively with the experimental data using racemic mixtures of (${\pm}$)-cis-4-acetamido-cyclopent-2-ene-1-ethyl acetate as substrates.

• Membrane Journal
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• v.28 no.1
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• pp.67-74
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• 2018

In the molecular dynamics study of polymeric membranes, it is very important to select the proper length of the polymer main chain because it requires a large number of constituent atoms and a long time to simulate the permeation behavior. In this study, we tried to investigate how the correlation between polymer main chain length and permeation behavior appears in actual molecular dynamics simulation results. Molecular dynamics were performed using the widely known commercial polymer Kapton(R) polyimide structure and the gas permeation behavior was simulated. The movement of the polymer main chain was not related to its length and the short main chain length did not act more actively. In addition, unlike the prediction that the end group of the polymer main chain is relatively easy to move, there are many cases where the atoms located at the middle of the polymer main chains have a higher movement than the atoms located at the end groups. Finally, permeabilities of the gas molecules was not affected by the length of the main chain and the end groups of the polymer, which indicates that the end effect should be carefully mentioned and followed by the verification process.

• Genomics & Informatics
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• v.3 no.3
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• pp.53-62
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• 2005

MicroRNAs play an important role in regulating gene expression, but their target identification is a difficult task due to their short length and imperfect complementarity. Burge and coworkers developed a program called TargetScan that allowed imperfect complementarity and established a procedure favoring targets with multiple binding sites conserved in multiple organisms. We improved their algorithm in two major aspects - (i) using well-defined UTR (untranslated region) database, (ii) examining the extent of conservation inside the 3' UTR specifically. Average length in our UTR database, based on the ECgene annotation, is more than twice longer than the Ensembl. Then, TargetScan was used to identify putative binding sites. The extent of conservation varies significantly inside the 3' UTR. We used the 'tight' tracks in the UCSC genome browser to select the conserved binding sites in multiple species. By combining the longer 3' UTR data, TargetScan, and tightly conserved blocks of genomic DNA, we identified 107 putative target genes with multiple binding sites conserved in multiple species, of which 85 putative targets are novel.

• Proceedings of the Korean Society of Dyers and Finishers Conference
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• 2008.10a
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• pp.77-78
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• 2008

Affinity between alkyl substituted super hydrophobic dyes and polypropylene fiber has been analyzed by using the molecular descriptor as a method to predict chemical and physical characteristics of compounds. Hydrophobicity of synthesized dyes calculated by LogP which is one of molecular descriptors was increased continuously as the length of alkyl substituents increased.