• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2000년도 International Symposium on Bioinformatics
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• pp.32-34
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• 2000

Computational chemistry is a discipline using computational methods for the calculation of molecular structure, properties, and reaction or for the simulation of molecular behavior. Relating and turning the complexity of data from genomics, high-throughput screening, combinatorial chemical synthesis, gene-expression investigations, pharmacogenomics, and proteomics into useful information and knowledge is the primary goal of bioinformatics. In particular, the structure-based molecular design is one of essential fields in bioinformatics and it can be called as structural bioinformatics. Therefore, the conformational analysis for proteins and peptides using the techniques of computational chemistry is expected to play a role in structural bioinformatics. There are two major computational methods for conformational analysis of proteins and peptides; one is the molecular orbital (MO) method and the other is the force field (or empirical potential function) method. The MO method can be classified into ab initio and semiempirical methods, which have been applied to relatively small and large molecules, respectively. However, the improvement in computer hardwares and softwares enables us to use the ab initio MO method for relatively larger biomolecules with up to v100 atoms or ∼800 basis functions. In order to show how computational chemistry can be used in structural bioinformatics, 1 will present on (1) cis-trans isomerization of proline dipeptide and its derivatives, (2) positional preference of proline in ${\alpha}$-helices, and (3) conformations and activities of Arg-Gly-Asp-containing tetrapeptides.

• 한국정보디스플레이학회:학술대회논문집
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• 한국정보디스플레이학회 2005년도 International Meeting on Information Displayvol.II
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• pp.1429-1431
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• 2005

Organic molecular-beam deposition of Mg:Ag thin films with a low Mg concentration on tris (8-hydroxyquinolino) aluminum $(Alq_3)$ layers at room temperature was performed to investigate the feasibility of using Mg:Ag thin films as cathode electrodes in organic light-emitting devices (OLEDs). The effective barrier height of the $Mg:Ag/Alq_3$ heterointerface, determined from current-voltage measurements, was as low as 0.23 eV. These results help improve understanding the electrical properties of the $Mg:Ag/Alq_3$ heterointerfaces in OLEDs.

• 한국컴퓨터그래픽스학회논문지
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• 제11권3호
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• pp.19-22
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• 2005

정보생물학 분야에 있어서 분자 구조를 3차원으로 렌더링하여 보여주는 것은 매우 중요한 작업이다. 특히 분자의 표면 렌더링은 분자의 3차원 구조 분석 등에 중요하게 사용된다. 그러나 분자 표면 렌더링을 수행하기 위해서는 많은 양의 폴리곤이 필요하게 된다. 특히 대장균 바이러스와 같은 분자량이 많은 거대 분자를 자연스럽게 렌더링 하기 위해서는 고가의 그래픽 전용 워크스테이션을 사용해야 한다. 본 논문에서는 저렴한 일반 PC 급 시스템에서도 거대 분자를 무리 없이 렌더링 할 수 있는 효율적인 알고리즘을 제안하였다. 제안하는 알고리즘은 높은 속도와 좋은 화질을 유지할 수 있는 Hybrid Point & Polygon 렌더링 기법이다. 이 알고리즘은 계층적인 자료구조인 옥트리(Octree)를 사용하였으며 최적의 성능을 내기 위하여 GPU가 작업을 처리한다. 제안된 알고리즘의 성능 평가는 일반 PC급에서 수행되었으며 특히 그래픽 카드 2개를 병렬로 연결하여 높은 성능을 낼 수 있는 SLI(Scalable Link Interface) 환경에서 평가를 수행하였다.

• Bulletin of the Korean Chemical Society
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• 제8권5호
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• pp.403-405
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• 1987

A dynamic laser light scattering system has been constructed using a personal computer. The intensity of the scattered light was detected with a photomultiplier tube and a photon counter. The BCD output of the photon counter which is proportional to the intensity of scattered light is fed into a personal computer via an interface card. The personal computer was programmed as an autocorrelator in machine language. The data acquisition rate of the system was about 600 samples/s which is adequate for studies on the molecular dynamics of concentrated polymer solutions, polymer latices with large particle size, and polymer glass systems. The constructed system was tested with polystyrene latex and the measured diameter of the latex particle agrees well with the supplier's value.

• Genomics & Informatics
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• 제4권4호
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• pp.161-166
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• 2006

The establishment of DNA microarray technology has enabled high-throughput analysis and molecular profiling of various types of cancers. By using the gene expression data from microarray analysis we are able to investigate diagnostic applications at the molecular level. The most important step in the application of microarray technology to cancer diagnostics is the selection of specific markers from gene expression profiles. In order to select markers of Immortalization and transformation we used c-myc and $H-ras^{V12}$ oncogene-transfected NIH3T3 cells as our model system. We have identified 8751 differentially expressed genes in the immortalization/transformation model by multivariate permutation F-test (95% confidence, FDR<0.01). Using the support vector machine algorithm, we selected 13 discriminative genes which could be used to predict immortalization and transformation with perfect accuracy. We assayed $H-ras^{V12}$-transfected 'transformed' cells to validate our immortalization/transformation dassification system. The selected molecular markers generated valuable additional information for tumor diagnosis, prognosis and therapy development.

• Journal of Information Processing Systems
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• 제11권2호
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• pp.248-265
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• 2015

In this paper, we propose a maximum entropy-based model, which can mathematically explain the bio-molecular event extraction problem. The proposed model generates an event table, which can represent the relationship between an event trigger and its arguments. The complex sentences with distinctive event structures can be also represented by the event table. Previous approaches intuitively designed a pipeline system, which sequentially performs trigger detection and arguments recognition, and thus, did not clearly explain the relationship between identified triggers and arguments. On the other hand, the proposed model generates an event table that can represent triggers, their arguments, and their relationships. The desired events can be easily extracted from the event table. Experimental results show that the proposed model can cover 91.36% of events in the training dataset and that it can achieve a 50.44% recall in the test dataset by using the event table.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2003년도 제2차 연례학술대회 발표논문집
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• pp.268-274
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• 2003

Most currently known molecular structures were determined by X-ray crystallography or Nuclear Magnetic Resonance (NMR). These methods generate a large amount of structure data, even far small molecules, and consist mainly of three-dimensional atomic coordinates. These are useful for analyzing molecular structure, but structure elements at higher level are also needed for a complete understanding of structure, and especially for structure prediction. Computational approaches exist for identifying secondary structural elements in proteins from atomic coordinates. However, similar methods have not been developed for RNA due in part to the very small amount of structure data so far available, and extracting the structural elements of RNA requires substantial manual work. Since the number of three-dimensional RNA structures is increasing, a more systematic and automated method is needed. We have developed a set of algorithms for recognizing secondary and tertiary structural elements in RNA molecules and in the protein-RNA structures in protein data banks (PDB). The present work represents the first attempt at extracting RNA structure elements from atomic coordinates in structure databases. The regularities in the structure elements revealed by the algorithms should provide useful information for predicting the structure of RNA molecules bound to proteins.

• 대한기계학회:학술대회논문집
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• 대한기계학회 2007년도 춘계학술대회A
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• pp.496-501
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• 2007

Recently, as MEMS and NEMS devices have been widely used in the various engineering applications, the characteristics of nanoscale systems are investigated in the limelight. However, as opposed to a macroscale system, the identification of the state of nanoscale systems is extremely hard because they can include only the order of $10^{3}\sim10^{5}$ molecules, which requires highly expensive and accurate experimental apparatus for an investigation. This limitations make the study on nanoscale system use computer simulations. Therefore, it is strongly required to identify the state of nanoscale system simulated in computer simulation. In these molecular dynamics(MD) study, we suggest that the potential energy of individual molecule can be used as criterion for defining the state of clusters or nanoscale systems. In addition, we compared the phase state from the potential energy with one from the radial distribution function(RDF) for verification. The comparison showed that the intermolecular potential energy can be used as a criteria distinguishing the phase state of nanoscale systems (This study will be published soon in the KSME transaction of the section B).

• 대한기계학회논문집B
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• 제31권5호
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• pp.435-447
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• 2007

Recently, as MEMS and NEMS devices have been widely used in the various engineering applications, the characteristics of nanoscale systems are investigated in the limelight. However, as opposed to a macroscale system, the identification of the state of nanoscale systems is extremely hard because they can include only the order of $10^3{\sim}10^5$ molecules, which requires highly expensive and accurate experimental apparatus for an investigation. This limitations make the study on nanoscale system use computer simulations. Therefore, it is strongly required to identify the state of nanoscale system simulated in computer simulation. In this molecular dynamics(MD) study, we suggest that the potential energy of individual molecule can be used as criterion for defining the state of clusters or nanoscale systems. In addition, we compared the phase state from the potential energy with one from the radial distribution function(RDF) for verification. The comparison showed that the intermolecular potential energy can be used as a criteria distinguishing the phase state of nanoscale systems.

• 한국정보과학회:학술대회논문집
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• 한국정보과학회 2007년도 한국컴퓨터종합학술대회논문집 Vol.34 No.1 (B)
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• pp.358-362
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• 2007

Glycomics와 Glycobiology는 Oligosaccharides와 Carbohydrate의 구조와 기능을 연구하기 위한 중요한 연구 방법이다. 현재 컴퓨터 시뮬레이션을 이용한 분자 모사 실험이 많은 연구 단체에 의해서 진행되고 있지만, 많은 컴퓨터 자원을 요구하는 문제로 인해서 활발하게 이루어 지지 않고 있는 실정이다. 현 시점에서 이러한 문제를 해결하기 위해서는 많은 자원과 오랜 시간을 소비해서 얻은 결과 데이터를 많은 과학자들에 의해서 공유하고 협업할 수 있는 시스템이 필요하다. Glyco-MGrid시스템은 분자 시뮬레이션 서비스 제공에 중점을 두고 있는 MGrid에서 생성되는 e-Clycomics 데이터들을 통합 관리하기 위한 사이버인프라스트럭쳐이다. 이 Glyco-MGrid는 분자 시뮬레이션의 결과를 통합 관리하기 위한 통합 데이터베이스 제공과 이를 통한 과학자들간의 협업을 지원하기 위해 그리드 기반의 e-Glycomics를 위한 공유, 통합 환경을 제공한다.