• Korean Journal of Materials Research
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• v.17 no.12
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• pp.637-641
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• 2007

The total energy and strength of Mg alloy doped with Al, Ca and Zn, were calculated using the density functional theory. The calculations was performed by two programs; the discrete variational $X{\alpha}\;(DV-X{\alpha})$ method, which is a sort of molecular orbital full potential method; Vienna Ab-initio Simulation Package (VASP), which is a sort of pseudo potential method. The fundamental mixed orbital structure in each energy level near the Fermi level was investigated with simple model using $DV-X{\alpha}$. The optimized crystal structures calculated by VASP were compared to the measured structure. The density of state and the energy levels of dopant elements was discussed in association with properties. When the lattice parameter obtained from this study was compared, it was slightly different from the theoretical value but it was similar to Mk, and we obtained the reliability of data. A parameter Mk obtained by the $DV-X{\alpha}$ method was proportional to electronegativity and inversely proportional to ionic radii. We can predict the mechanical properties because $\Delta{\overline{Mk}}$is proportional to hardness.

• Proceedings of the Korean Society for Cognitive Science Conference
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• 2005.05a
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• pp.130-134
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• 2005

본 연구는 애너그램(anagram) 문제해결 과제에서 발생하는 제약들(영어 철자연쇄 집합의 출현 확률과 단어 내 위치 확률)을 동시에 병렬적으로 만족시키는 확률 모델 학습과정을 보인다. 애너그램에 관한 많은 선행연구들은 이 문제해결 과정이 단순히 기호처리적인 층위뿐만 아니라 하위기호적(subsymbolic) 층위에서의 상향식 처리로 인해 일어남을 밝혀왔고, 주로 영어 철자의 연쇄체의 확률값을 이용해왔다. 본 연구는 확률 라이브러리 모델(Probabilistic Library Model)을 통해 애너그램 문제해결이 한 번씩 끝날 때마다 철자 연쇄체의 출현 및 위치 분포 확률이 어떻게 유연한 변화를 갖는지에 집중한다. 하나의 문제를 풀고 나면 본 모델은 그 전 문제를 풀었을 때의 상태 패턴으로부터 변화를 보인다. 이러한 분포 변화를 통해 하위기호적 활동의 영향이 문제해결에 있어서 학습구조의 유연한 변화에 중요한 영향을 끼친다는 점을 확인했다.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.3-3
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• 2003

With biomedical literature expanding so rapidly, there is an urgent need to discover and organize knowledge extracted from texts. Although factual databases contain crucial information the overwhelming amount of new knowledge remains in textual form (e.g. MEDLINE). In addition, new terms are constantly coined as the relationships linking new genes, drugs, proteins etc. As the size of biomedical literature is expanding, more systems are applying a variety of methods to automate the process of knowledge acquisition and management. In my talk, I focus on the project, GENIA, of our group at the University of Tokyo, the objective of which is to construct an information extraction system of protein - protein interaction from abstracts of MEDLINE. The talk includes (1) Techniques we use fDr named entity recognition (1-a) SOHMM (Self-organized HMM) (1-b) Maximum Entropy Model (1-c) Lexicon-based Recognizer (2) Treatment of term variants and acronym finders (3) Event extraction using a full parser (4) Linguistic resources for text mining (GENIA corpus) (4-a) Semantic Tags (4-b) Structural Annotations (4-c) Co-reference tags (4-d) GENIA ontology I will also talk about possible extension of our work that links the findings of molecular biology with clinical findings, and claim that textual based or conceptual based biology would be a viable alternative to system biology that tends to emphasize the role of simulation models in bioinformatics.

• BMB Reports
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• v.37 no.1
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• pp.83-92
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• 2004

As a result of the enormous amount of information that has been collected with E. coli over the past half century (e.g. genome sequence, mutant phenotypes, metabolic and regulatory networks, etc.), we now have detailed knowledge about gene regulation, protein activity, several hundred enzyme reactions, metabolic pathways, macromolecular machines, and regulatory interactions for this model organism. However, understanding how all these processes interact to form a living cell will require further characterization, quantification, data integration, and mathematical modeling, systems biology. No organism can rival E. coli with respect to the amount of available basic information and experimental tractability for the technologies needed for this undertaking. A focused, systematic effort to understand the E. coli cell will accelerate the development of new post-genomic technologies, including both experimental and computational tools. It will also lead to new technologies that will be applicable to other organisms, from microbes to plants, animals, and humans. E. coli is not only the best studied free-living model organism, but is also an extensively used microbe for industrial applications, especially for the production of small molecules of interest. It is an excellent representative of Gram-negative commensal bacteria. E. coli may represent a perfect model organism for systems biology that is aimed at elucidating both its free-living and commensal life-styles, which should open the door to whole-cell modeling and simulation.

• Proceedings of the Korean Vacuum Society Conference
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• 2013.02a
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• pp.645-645
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• 2013

Applying a first-principles computational approach combining density-functional theory and matrix Green's function calculations, we have studied the effects [2+2] cycloaddition olligormerization of fullerene $C_{60}$ chains on their junction charge transport properties. Analyzing first the microscopic mechanism of the switching realized in recent scanning tunneling microscope (STM) experiments, we found that, in agreement with experimental conclusions, the device characteristics are not significantly affected by the changes in electronic structure of $C_{60}$ chains. It is further predicted that the switching characteristics will sensitively depend on the STM tip metal species and the associated energy level bending direction in the $C_{60}-STM$ tip vacuum gap. Considering infinite $C_{60}$ chains, however, we confirm that unbound $C_{60}$ chains with strong orbital hybridizations and band formation should in principle induce a much higher conductance state. We demonstrate that a nanoelectromechanical approach in which the $C_{60}-STM$ tip distance is maintained at short distances can achieve a metal-independent and drastically improved switching performance based on the intrinsically better electronic connectivity in the bound $C_{60}$ chains.

• Journal of Biomedical Engineering Research
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• v.28 no.3
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• pp.377-386
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• 2007

Mechanical loading to bone cells using simple sine wave or constant wave fluid flow has been widely used for in vitro experiments. Human gait is characterized by a complex loading to bones of lower extremities which results from a series of events consisting of heel strike, foot flat and push-off during the stance phase of the gait cycle. Telemetric force analyses have shown that human femora are subject to multiphasic loading. Therefore, it would be ideal if the physiologic loading conditions during human walking can be used for in vitro mechanotransduction studies. Here, for a mechanotransduction study, we develop it fluid flow system (FFS) in order to simulate human physiologic mechanicalloading on bone cells. The development methods of the FFS including the COR (Center for Orthopedic Research), monitor program are presented. The FFS could generate various multiphasic loading conditions of human gaits with output flow. Wall shear distribution was very uniform, with 81 % of the effective loading area of the culture on a glass slide. Our results demonstrated that the FFS, provide a new translational approach for unveiling molecular mechanotransduction pathways in bone cells.

• Journal of the Korean Institute of Electrical and Electronic Material Engineers
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• v.19 no.2
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• pp.116-125
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• 2006

We have presented a nanoelectromechanical (NEM) model based on atomistic simulations. Our models were applied to a NEM device as called a nanotube random access memory (NRAM) operated by an atomistic capacitive model including a tunneling current model. We have performed both static and dynamic analyses of a NRAM device. The turn-on voltage obtained from molecular dynamics simulations was less than the half of the turn-on voltage obtained from the static simulation. Since the suspended carbon nanotube (CNT) oscillated with the amplitude for the oscillation center under an externally applied force, the quantity of the CNT-gold interaction in the static analysis was different from that in the dynamic analysis. When the gate bias was applied, the oscillation centers obtained from the static analysis were different from those obtained from the dynamics analysis. Therefore, for the range of the potential difference that the CNT-gold interaction effects in the static analysis were negligible, the vibrations of the CNT in the dynamics analysis significantly affected the CNT-gold interaction energy and the turn-on voltage. The turn-on voltage and the tunneling resistance obtained from our tunneling current model were in good agreement with previous experimental and theoretical works.

• Journal of ILASS-Korea
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• v.16 no.4
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• pp.167-175
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• 2011

The HCCI engines have been known with high efficiency and low pollution and can be actualized as the new internal combustion engines. However, As for(??) the ignition and combustion depend strongly on the oxidation reaction of the fuel, so it is difficult to control auto-ignition timing and combustion duration. Purpose of this paper is creating the database for development of multi-dimensional simulation and investigating the influence of different molecular structure. In this research, the effect of n-heptane mole ratio in fuel (XnH) on the ignition delay from homogeneous charge compression ignition(HCCI) has been investigated experimentally. By varying the XnH, it was possible to ascertain whether or not XnH is the main resource of ignition delay. Additionally, the information on equivalence ratio for varying XnH was obtained. The tests were performed on a RCM (Rapid Compression Machine) fueled with n-heptane and iso-octane. The results showed that decreasing XnH (100, 30, 20, 10,0), the ignition delays of low temperature reaction (tL) and high temperature reaction (tH) is longer. And the temperature of reaction increases by about 30K. n-heptane partial equivalence ratio (fnH) affect on tL.and TL. When ${\phi}$nH was increased as a certain value, tL was decreased and TL was increased.

• Bulletin of the Korean Chemical Society
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• v.34 no.12
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• pp.3703-3708
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• 2013

The scaling relationship of the longest relaxation time of a single chain of semiflexible biological polyelectrolyte has been investigated by performing well-established coarse-grained Brownian dynamics simulations. Two kinds of longest relaxation times were estimated from time-sequences of chain trajectories, and their behaviors were interpreted by applying the scaling law for different molecular weights of polyelectrolyte and Debye lengths. The scaling exponents for longest stress relaxation and rotational relaxation are found in the ranges of 1.67-1.79 and 1.65-1.81, respectively, depending on the physicochemical interaction of electrostatic Debye screening. The scaling exponent increases with decreasing screening effect, which is a special feature of polyelectrolytes differing from neutral polymers. It revealed that the weak screening allows a polyelectrolyte chain to follow the behavior in good solvent due to the strong electrostatic repulsion between beads.

• 한국정보디스플레이학회:학술대회논문집
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• 2006.08a
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• pp.121-124
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• 2006

A novel quantum chemical molecular dynamics program, 'Colors' was developed to simulate the electronic structure of rare earth-doped phosphor materials as well as the destruction processes of MgO protecting layer in plasma display panel (PDP). We have also developed a quantitative prediction method based on Monte Carlo simulation technique to evaluate the electrical conductivity of insulators, semiconductors, and metals as well as the spatial distribution of electron density by Colors code. All these original simulators enable us to study theoretically a variety of materials related to PDP.