• 셀메드
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• 제6권4호
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• pp.24.1-24.4
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• 2016

The emergence of influenza virus and antigenic drift are potential cause of world-wide pandemic. There are some commercially available drugs in the market to treat influenza. During past decade, however, critical resistances have been raised for biological targets. Because of structural complexity and flexibility of target proteins, applying a computational modeling tool is very beneficial for developing alternative anti-influenza drugs. In this review, we introduced molecular dynamics (MD) simulations approach to reflect full conformational flexibility of proteins during molecular modeling works. Case studies of MD works were summarized for the drug discovery and drug resistance mechanism of anti-influenza pharmaceuticals.

• 셀메드
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• 제2권4호
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• pp.30.1-30.4
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• 2012

Traditional Chinese medicine classifies peripheral nerve impairment as paralysis and arthromyodynia, and considers that it is the result of defects of meridians and vessels, QI and blood, bones and muscles. Huangqi (Astragalus) Guizhi (Cassia Twig) Wuwu Tang, as a Qi invigorating formula, is usually used to improve peripheral nerve impairment. In recent years, some scholars have conducted research into Chemotherapy-induced peripheral neuropathy (CIPN) treatment with Huangqi Guizhi Wuwu Tang and certain values of this treatment approach have been identified. CIPN is a type of blood-arthralgia Zheng in traditional Chinese medicine theory. In this review, we will discuss the treatment of CIPN with Huangqi Guizhi Wuwu Tang according to blood-arthtalgia Zheng.

• Tuberculosis and Respiratory Diseases
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• 제75권5호
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• pp.181-187
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• 2013

The emergence of new therapeutic agents for non-small cell lung cancer (NSCLC) implies that histologic subtyping and molecular predictive testing are now essential for therapeutic decisions. Histologic subtype predicts the efficacy and toxicity of some treatment agents, as do genetic alterations, which can be important predictive factors in treatment selection. Molecular markers, such as epidermal growth factor receptor (EGFR) mutation and anaplastic lymphoma kinase (ALK) rearrangement, are the best predictors of response to specific tyrosine kinase inhibitor treatment agents. As the majority of patients with NSCLC present with unresectable disease, it is therefore crucial to optimize the use of tissue samples for diagnostic and predictive examinations, particularly for small biopsy and cytology specimens. Therefore, each institution needs to develop a diagnostic approach requiring close communication between the pulmonologist, radiologist, pathologist, and oncologist in order to preserve sufficient biopsy materials for molecular analysis as well as to ensure rapid diagnosis. Currently, personalized medicine in NSCLC is based on the histologic subtype and molecular status. This review summarizes strategies for tissue acquisition, histologic subtyping and molecular analysis for predictive testing in NSCLC.

• BMB Reports
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• 제39권6호
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• pp.766-773
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• 2006

Fragile-X-syndrome (FXS) is the most common type of inherited cognitive impairment. The underlying molecular alteration consists of a CGG-repeat amplification within the FMR-1 gene. The phenotype is only apparent once a threshold in the number of repeats has been exceeded (full mutation). The aim of this study was to characterize the FMR-1 CGG-repeat status in Argentine patients exhibiting mental retardation. A total of 330 blood samples from patients were analyzed by PCR and Southern blot analysis. Initially, DNA from 78 affected individuals were studied by PCR. Since this method is unable to detect high molecular weight alleles, however, we undertook a second approach using the Southern blotting technique to analyze the CGG repeat number and methylation status. Southern blot analysis showed an altered pattern in 14 out of 240 (6%) unrelated patients, with half of them presenting a mosaic pattern. Eight out of 17 families (47%) showed a (suggest deleting highlight). The characteristic FXS pattern was identified in 8/17 families (47%), and in 4 of these families 25% of the individuals presented with a mosaic model. The expansion from pre-mutation to full mutation was shown to occur both at the pre and post zygotic levels. The detection of FXS mutations has allowed us to offer more informed genetic counseling, prenatal diagnosis and reliable patient follow-up.

• 한국연소학회:학술대회논문집
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• 대한연소학회 2003년도 제27회 KOSCO SYMPOSIUM 논문집
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• pp.57-61
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• 2003

In the combustion modeling of non-premixed flames, the mixture fraction conserved scalar approach is widely utilized because reactants are mixed at the molecular level before burning and atomic elements are conserved in chemical reactions. In the mixture fraction approach, combustion process is simplified to a mixing problem and the interaction between chemistry and turbulence could be modelled by many sophisticated combustion models including the flamelet model and CMC. However, most of the mixture fraction approach is restricted to one mixture system. In this study, the flamelet model based on the two-feed system is extended to the multiple fuel-feeding systems by the two mixture fraction conserved scalar approach.

• Asian-Australasian Journal of Animal Sciences
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• 제17권6호
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• pp.877-884
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• 2004

Although gut microbial functions have been analyzed through cultivation of isolated microbes, molecular analysis without cultivation is becoming a popular approach in recent years. Gene cloning studies have partially revealed the mechanisms involved in fiber digestion of individual microbe. The molecular approach finally made it possible to analyze full genomes of the representative rumen cellulolytic bacteria Fibrobacter and Ruminococcus. The coming database may contain useful information such as regulation of gene expression relating to fiber digestion. Meanwhile, unculturable bacteria are still poorly characterized, even though they are main constituents of gut microbial ecosystem. The molecular analysis is essential to initiating the studies on these unculturable bacteria. The studies dealing with rumen and large intestine are revealing considerable complexity of the microbial ecosystems with many undescribed bacteria. These bacteria are being highlighted as possibly functional members contributing to feed digestion. Manipulation of gut bacteria and gut ecology for improving animal production is still at challenging stage. Bacteria newly introduced in the rumen, whether they are genetically modified or not, suffer from poor survival. In one of these attempts, Butyrivibrio fibrisolvens expressing a foreign dehalogenase was successfully established in sheep rumen to prevent fluoroacetate poisoning. This expands choice of forages in tropics, since many tropic plants are known to contain the toxic fluoroacetate. This example may promise the possible application of molecular breeding of gut bacteria to the host animals with significance in their health and nutrition. When inoculation strategies for such foreign bacteria are considered, it is obvious that we should have more detailed information of the gut microbial ecology.

• 한국전산구조공학회논문집
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• 제26권5호
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• pp.393-399
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• 2013

본 논문은 그래핀의 모드 I 균열 진전에 대한 분자동역학 해석과 수치보조장을 사용하는 영역 투영 방법의 역문제 해석 방법을 결합하여 균열 선단 응집 법칙을 평가하는 효율적인 방법을 제시하고 있다. 그래핀의 균열 선단 응집 법칙을 결정하는 것은 균열 선단에서 멀리 떨어진 영역의 변위를 사용하여 균열 면에서 미지의 응집 트랙션과 열림 변위를 구하는 역문제를 해석해야 하는데 상호 J-적분과 M-적분의 경로 보존성과 효율적인 수치보조장을 사용하는 방법을 적용하였다. 분자동역학 해석에서 원자 변위를 유한요소 절점 변위로 이동최소자승법을 사용하여 근사하였으며 안정적인 역문제 해석을 통하여 원자 단위의 거동을 연속체 해석으로 연결시킬 수 있는 새로운 방법을 보여주었다.

• Bulletin of the Korean Chemical Society
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• 제32권11호
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• pp.4027-4034
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• 2011

$CaCO_3$ crystalline structures having novel assemblies were in situ fabricated as analogs of naturally occurring proteins and polysaccharides for biomineralization. The calcite crystal was mineralized in a poly(vinyl alcohol)-$Ca^{2+}$ complex film immersed in a $Na_2CO_3$ solution containing poly(aspartic acid). The morphology and size of the $CaCO_3$ crystals were tuned by varying the concentration of poly(aspartic acid). The mechanisms of their nucleation orientation and formation were investigated experimentally and through molecular dynamics (MD) simulations in order to obtain a better understanding of the interactions between the polymers and the crystal at the molecular level. Both the MD results and experimental results indicate that the interaction between PVA and calcite mainly depends on the concentration of the polymer. The novel approach proposed herein for the fabrication of inorganic crystalline assembly structures can be used to fabricate precise crystalline structures.

• Advances in nano research
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• 제3권3호
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• pp.143-168
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• 2015

Initiation of crack and its growth simulation requires accurate model of traction - separation law. Accurate modeling of traction-separation law remains always a great challenge. Atomistic simulations based prediction has great potential in arriving at accurate traction-separation law. The present paper is aimed at establishing a method to address the above problem. A method for traction-separation law prediction via utilizing atomistic simulations data has been proposed. In this direction, firstly, a simpler approach of common neighbor analysis (CNA) for the prediction of crack growth has been proposed and results have been compared with previously used approach of threshold potential energy. Next, a scheme for prediction of crack speed has been demonstrated based on the stable crack growth criteria. Also, an algorithm has been proposed that utilizes a variable relaxation time period for the computation of crack growth, accurate stress behavior, and traction-separation atomistic law. An understanding has been established for the generation of smoother traction-separation law (including the effect of free surface) from a huge amount of raw atomistic data. A new curve fit has also been proposed for predicting traction-separation data generated from the molecular dynamics simulations. The proposed traction-separation law has also been compared with the polynomial and exponential model used earlier for the prediction of traction-separation law for the bulk materials.

• Structural Engineering and Mechanics
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• 제30권2호
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• pp.177-190
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• 2008

Material failure behavior is generally dependent on loading rate. Especially in brittle and quasi-brittle materials, rate dependent material behavior can be significant. Empirical formulations are often used to predict the rate dependency, but such methods depend on extensive experimental works and are limited by practical constraints of physical testing. Numerical simulation can be an effective means for extracting knowledge about rate dependent behavior and for complementing the results obtained by testing. In this paper, the failure behavior of a brittle material under different loading rates is simulated by molecular dynamics analysis. A notched specimen is modeled by sub-million particles with a normalization scheme. Lennard-Jones potential is used to describe the interparticle force. Numerical simulations are performed with six different loading rates in a direct tensile test, where the loading velocity is normalized to the ratio of the pseudo-sonic speed. As a consequence, dynamic features are achieved from the numerical experiments. Remarkable failure characteristics, such as crack surface interaction/crack arrest, branching, and void nucleation, vary in case of the six loading cases. These characteristics are interpreted by the energy concept approach. This study provides insight into the change in dynamic failure mechanism under different loading rates.