• Multiscale and Multiphysics Mechanics
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• v.1 no.1
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• pp.53-64
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• 2016

Amyloid fibrils have recently been considered as an interesting material, since they exhibit the excellent mechanical properties such as elastic modulus in the order of 10 GPa, which is larger than that of other protein materials. Despite recent findings of these excellent mechanical properties for amyloid fibrils, it has not been fully understood how these excellent mechanical properties are achieved. In this work, we have studied the nanomechanical deformation behaviors and properties of amyloid fibrils such as their elastic modulus as well as fracture strength, by using atomistic simulations, particularly steered molecular dynamics simulations. Our simulation results suggest the important role of the length of amyloid fibrils in their mechanical properties such that the fracture force of amyloid fibril is increased when the fibril length decreases. This length scale effect is attributed to the rupture mechanisms of hydrogen bonds that sustain the fibril structure. Moreover, we have investigated the effect of boundary condition on the nanomechanical deformation mechanisms of amyloid fibrils. It is found that the fracture force is critically affected by boundary condition. Our study highlights the crucial role of both fibril length and boundary condition in the nanomechanical properties of amyloid fibrils.

• Journal of Animal Science and Technology
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• v.53 no.3
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• pp.195-202
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• 2011

Maintenance of adequate telomere length in developing cells is the most important concern to preserve the integrity of the genome. The length of telomere is strictly regulated by numerous telomere-binding proteins and/or interacting factors. Even though the expression of telomerase in the male reproductive tract has been characterized, developmental expressional profiling of telomerase and other telomere-associated proteins has not been determined in detail. The present study was attempted to examine expression patterns of catalytic subunit (Tert) and RNA component (Terc) of telomerase and two telomerase associated factors, telomerase associated protein 1 (Tep1) and TERF1 (TRF1) interacting nuclear factor 2 (Tinf2) in the testis and seminal vesicle of male rat during postnatal development. The real-time PCR analysis was utilized to quantify mRNA expression of molecules. The abundance of Tep1 mRNA in the testis and seminal vesicle was the highest at 5 months of age. Expressional fluctuation of Tinf2 during postnatal development was found in the testis, while expression of Tinf2 in the seminal vesicle was gradually increased until 5 months of age and then significantly decreased later. mRNA level of Tert gene in the testis was significantly increased at the adult and the elder, while the highest expression of Tert gene in the seminal vesicle was found at 5 months of age. Expression of Terc transcript in the testis and seminal vesicle was the highest at 5 months of age, followed by significant reduction at 1 and 2 years of ages. Such differential gene expression of telomere-associated factors and telomerase components in different male reproductive tissues during postnatal development indicates that maintenance of telomere length would be regulated in tissue- and/or age-specific manners.

• Korean Journal of Food Science and Technology
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• v.27 no.5
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• pp.757-761
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• 1995

The relationship between the molecular structure of rice starch and the texture of cooked rice was investigated using hot-water soluble rice starch. The structure of hot-water soluble starch bound amylose which was composed of small molecular weight and amylopectin which was composed of chain length of $\overline{DP}\;10{\sim}20$, and the average composition of amylose : amylopectin was 7 : 3. The molecular weight of amylose was the smaller and super long chain of amylopectin was the fewer, the extractable ratio of hot-water soluble rice starch was the higher. And hot-water solubility of rice starch be responsible for molecular structure of starch. On the texture of cooked rice, the extractable ratio of hot-water soluble rice starch was the higher, the hardness was the lower and the adhesiveness was the higher. The results suggest that the molecular structure of rice starch could be responsible for the texture of cooked rice.

• Korean Journal of Microbiology
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• v.48 no.3
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• pp.200-206
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• 2012

A bacterial strain capable of synthesizing polyhydroxyalkanoates (PHAs) with an unusual pattern of monomer units was isolated from activated sludge using the enrichment culture technique. The organism, identified as Pseudomonas aeruginosa P-5, produced polyesters consisting of 3-hydroxyvalerate and medium-chain-length (MCL) 3-hydroxyalkanoate monomer units when $C_{-odd}$ alkanoic acids such as nonanoic acid and heptanoic acid were fed as the sole carbon source. Solvent fractionation experiments using chloroform and hexane revealed that the 3-hydroxyalkanoate monomer units in these polyesters were copolymerized. The molar concentration of 3-hydroxyvalerate in the polyesters produced were significantly elevated up to 26 mol% by adding 1.0 g/L valeric acid as the cosubstrate. These copolyesters were sticky with low degrees of crystallinity. The PHA synthase genes were cloned, and the deduced amino acid sequences were determined. P. aeruginosa P-5 possessed genes encoding MCL-PHA synthases (PhaC1 and PhaC2) but lacked the short-chain-length PHA synthase gene, suggesting that the MCL-PHA synthases from P. aeruginosa P-5 are uniquely active for polymerizing (R)-3-hydroxyvaleryl-CoA as well as MCL (R)-3-hydroxyacyl-CoAs.

• Transactions of the Korean Society of Mechanical Engineers B
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• v.40 no.10
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• pp.659-666
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• 2016

A numerical study, using the molecular dynamics simulation method, was carried out to investigate the wetting characteristics of water droplets on a solid square pillar surface with variable periodic edge length patterns at the nanoscale. In this study, the pillar plane was supposed to be rectangular or square shaped. In addition, the surface area was increased while the shape of the pillar plane was kept fixed. In the case of the square pillar, the edge length increased from $4.24{\AA}$ to $12.72{\AA}$. Also, the rectangular pillar had two types of length edges. In this case, one edge length was fixed at $8.48{\AA}$ and the other edge length was increased from $4.24{\AA}$ to $12.72{\AA}$. Through these length changes, the hydrophobicity and hydrophilicity of a water droplet on the variable pillar surfaces were analyzed.

• Interaction and multiscale mechanics
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• v.4 no.3
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• pp.219-237
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• 2011

Recent advances in scientific computing enable the full atomistic simulation of DNA molecules. However, there exists length and time scale limitations in molecular dynamics (MD) simulation for large DNA molecules. In this work, a two-level homogenization of DNA molecules is proposed. A wavelet projection method is first introduced to form a coarse-grained DNA molecule represented with superatoms. The coarsened MD model offers a simplified molecular structure for the continuum description of DNA molecules. The coarsened DNA molecular structure is then homogenized into a three-dimensional beam with embedded molecular properties. The methods to determine the elasticity constants in the continuum model are also presented. The proposed continuum model is adopted for the study of mechanical behavior of DNA loop.

• Journal of Nutrition and Health
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• v.29 no.2
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• pp.153-158
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• 1996

Polyethylene glycols(PEGs)are hydrophilic molecules that have been used to characterize intestinal permeability via the paracellular pathway. Using a mixture of PEGs(400, 600 and 1000), containing oligomers in the molecular weight range 330 to 1122 D, the molecular weight permeability dependence in the jejunum of the rat small intestine was examined, employing an in situ recirculation perfusion technique. Individual oligomers were determined by HPLC with refractive detection. In the range studied, a distinct molecular weight cut-off was not apparent. Corrected for the length of jejunum used in the study, over the molecular weight range 330 to 1122D, the apparent permeability(Papp) of PEG ranged from 4.92$\pm$0.02$\times$10-5cm/sec(mean$\pm$SEM, n=5) to 0.28$\times$10-5cm/sec. Also, it was observed that the apparent permeability was inversely proportional to approximately MW2. The results in this study suggest that molecular weight is an important factor in determining the intestinal permeability.

• Asian-Australasian Journal of Animal Sciences
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• v.22 no.9
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• pp.1241-1247
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• 2009

A large number of branded chicken products exist in Japan, and in some cases, the breed of chicken is an important factor used to attract consumer interest in the retail product. In order to establish a simple method for verifying such breed claims we applied the amplified fragment length polymorphism (AFLP) technique to nine chicken breeds (White Cornish, Red Cornish, White Plymouth Rock, New Hampshire, Rhode Island Red, Barred Plymouth Rock, Hinaidori, Tosajidori, Tsushimajidori) to search for molecular markers able to discriminate chicken breeds. Three breed-specific single nucleotide polymorphisms (SNP) were identified, one for each of Hinaidori, Tosajidori, or New Hampshire. A total of 219 individuals from the nine breeds were analyzed using a specific PCR test for each of these SNP. The PCR tests made it possible to discriminate between the breeds of chickens to identify products from these three breeds. This PCR method provides an efficient method for the routine analysis and verification of certified chicken products.

• Bulletin of the Korean Chemical Society
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• v.35 no.9
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• pp.2679-2683
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• 2014

Mechanisms underlying the impacts of interactions between carbon nanoparticles (CNPs) and ionic liquids (ILs) on the physicochemical behavior of CNPs need to be more full worked out. This manuscript describes a theoretical investigation at multiple levels on the interactions of fullerene $C_{60}$ with 21 imidazolium-based ILs of varying alkyl side chain lengths and anionic types and their impacts on $C_{60}$ dispersion behavior. Results show that ${\pi}$-cation interaction contributed to mechanism of the $C_{60}$-IL interaction more than ${\pi}$-anion interaction. The calculated interaction energy ($E_{INT}$) indicates that $C_{60}$ can form stable complex with each IL molecule. Moreover, the direction of charge transfer occurred from IL to $C_{60}$ during the $C_{60}$-IL interaction. Quantitative models were developed to evaluate the self-diffusion coefficient of $C_{60}$ ($D_{fullerene}$) in bulk ILs. Three interpretative molecular descriptors (heat of formation, $E_{INT}$, and charge) that describe the $C_{60}$-IL interactions and the alkyl side chain length were found to be determinants affecting $D_{fullerene}$.

• Fibers and Polymers
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• v.4 no.1
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• pp.15-19
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• 2003

The self-assembly of asymmetric ABC triblock copolymers in the ordered structure is investigated using an isothermal-isobaric molecular dynamics simulation. Unlike symmetric A BC triblock copolymers, more fascinating mophologies are observed in asymmetric ones because of a larger difference of incompatibility between the components. Various modes of self-assembly in assymmetric ABC triblock copolymers are also observed depending on the block composition. When the composition of block A Is changed from 0.125: to 0.25 at the same $f_B$ : 0.25, the morphological transition from the “cylinder in cylinder” to “cylinders at cylinder” structure is observed in the simulation. In the case of ABC triblocks with $f_B$=0.5, a lamellar-type structure is changed to a cylinder-type structure with increasing the length of block A. When the midblock length increases further to $f_B$=0.625, the “spheres on cylinder” structure is observed in both the $A_{10}$$B_{50}$$C_{20}$ and $A_{20}$$B_{50}$$C_{10}$ triblocks. From these results, the phase diagram of ABC triblock copolymers can be constructed.