Computational Three-Residue Fragment Assembly and Folding Optimization for Protein Structure Design

정민중 한국물리학회 2009 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.55 No.5

Computational modeling of the unique tertiary structure of a protein from its amino acid sequence alone is one of the important challenges in science and technology. The tertiary structure itself and the folding mechanism toward it are indispensable for understanding the function and the biological role of the protein. One of the computational methods often used for this modeling is the fragment assembly method because it shows good structural modeling performance in many cases. There are limitations, however, in the conventional fragment assembly methods. Arguments for uses of energy functions and global optimization to predict the structures are in progress, for example. In this study, a new modeling method to predict protein tertiary structures is proposed. The proposed system mainly consists of two methods. The first one is a fragment assembly, in which 3-residue fragments of representative protein chains are used to produce prototypes of a given sequence of amino acids. The second one is global optimization, which uses folding optimization to construct final protein structures. One of our computational models of the protein, which yielded a 5.15 °A root mean square deviation for its native tertiary structure, is provided with other experiments. Computational modeling of the unique tertiary structure of a protein from its amino acid sequence alone is one of the important challenges in science and technology. The tertiary structure itself and the folding mechanism toward it are indispensable for understanding the function and the biological role of the protein. One of the computational methods often used for this modeling is the fragment assembly method because it shows good structural modeling performance in many cases. There are limitations, however, in the conventional fragment assembly methods. Arguments for uses of energy functions and global optimization to predict the structures are in progress, for example. In this study, a new modeling method to predict protein tertiary structures is proposed. The proposed system mainly consists of two methods. The first one is a fragment assembly, in which 3-residue fragments of representative protein chains are used to produce prototypes of a given sequence of amino acids. The second one is global optimization, which uses folding optimization to construct final protein structures. One of our computational models of the protein, which yielded a 5.15 °A root mean square deviation for its native tertiary structure, is provided with other experiments.

저침습 의료기술과 정밀공학 마이크로·나노머시닝 기술을 이용한 저침습 의료기기의 개발

정민중,芳賀洋一(Yoichi HAGA),松永忠雄(Tadao MATSUNAGA),江刺正喜(Masayoshi ESASHI) (사)한국CDE학회 2009 한국CAD/CAM학회학회지 Vol.15 No.2

A decentralized approach to damage localization through smart wireless sensors

정민중,고봉환 국제구조공학회 2009 Smart Structures and Systems, An International Jou Vol.5 No.1

This study introduces a novel approach for locating damage in a structure using wireless sensor system with local level computational capability to alleviate data traffic load on the centralized computation. Smart wireless sensor systems, capable of iterative damage-searching, mimic an optimization process in a decentralized way. The proposed algorithm tries to detect damage in a structure by monitoring abnormal increases in strain measurements from a group of wireless sensors. Initially, this clustering technique provides a reasonably effective sensor placement within a structure. Sensor clustering also assigns a certain number of master sensors in each cluster so that they can constantly monitor the structural health of a structure. By adopting a voting system, a group of wireless sensors iteratively forages for a damage location as they can be activated as needed. Since all of the damage searching process occurs within a small group of wireless sensors, no global control or data traffic to a central system is required. Numerical simulation demonstrates that the newly developed searching algorithm implemented on wireless sensors successfully localizes stiffness damage in a plate through the local level reconfigurable function of smart sensors.

균열면에 작용하는 내압과 열전달의 영향을 고려한 노즐부의 응력확대계수 해석

정민중,김영진,강기주,범현규,표창률,Jeong, Min-Jung,Kim, Yeong-Jin,Gang, Gi-Ju,Beom, Hyeon-Gyu,Pyo, Chang-Ryul 대한기계학회 2000 大韓機械學會論文集A Vol.24 No.9

In order to investigate the effect of nozzle on stress concentration in pressure vessels, three dimensional finite element analyses were performed. The results were compared with those for corresponding two dimensional axisymmetric finite element analyses. A three dimensional finite element model with a surface crack was also designed to evaluate the effect of internal pressure and heat transfer on crack face, and the resulting stress intensity factors from the finite element analyses were compared with those for ASME Sec. XI and Raju-Newman's stress intensity factor solution. As a result, the validity of currently available stress intensity factor solutions for a surface crack was reviewed in the presence of geometrical complexity, heat transfer and internal pressure.

웹기반 대용량 계산환경 구축 및 응용연구

정민중,김병상,Jeong, Min-Joong,Kim, Byung-Sang 한국전산구조공학회 2007 한국전산구조공학회논문집 Vol.20 No.3

공학 및 과학문제 해석을 위해 적용되는 전산 시뮬레이션은 다양한 변수 혹은 데이터의 변화를 통해 다수의 작업을 생성하고 계산함과 동시에, 생성된 결과를 비교 분석하기 위한 필수적인 기법이다. 본 연구에서는 그리드 컴퓨팅을 활용하여 웹상에서 대용량의 전산 시뮬레이션이 가능한 시스템을 개발하고, 이를 이용한 2가지 실제 응용사례를 제시한다. 첫 번째 응용사례는 e-AIRS(Aerospace Integrated Research Environment)라 명명된 연구포탈이다 e-AIRS는 수치해석 연구자가 대규모의 전산 해석을 실시하고, 실험 연구자가 원격지에서 실험을 요청하고 그 결과를 모니터링 할 수 있는 e-Science 연구환경을 제공한다. 두 번째 응용사례는 대규모 계산환경을 이용한 단백질 구조설계를 제시한다. 제안된 계산환경을 이용하여 생성된 단백질 전산 예측구조와 자연상태 구조를 비교하고, 제안된 계산환경의 유용성을 검토한다. Many engineering problems often require the large amount of computing resources for iterative simulations of problems treating many parameters and input files. In order to overcome the situation, this paper proposes an e-Science based computational system. The system exploits the Grid computing technology to establish an integrated web service environment which supports distributed high throughput computational simulations and remote executions. The proposed system provides an easy-to-use parametric study service where a computational service includes real time monitoring. To verify usability of the proposed system, two kinds of applications were introduced. The first application is an Aerospace Integrated Research System (e-AIRS). The e-AIRS adapts the proposed computational system to solve CFD problems. The second one is design and optimization of protein 3-dimensional structures in structural biology.

가상현실 기반 건전성평가시스템 개발 ( 원자력발전소에의 적용 ) ( Development of Virtual Reality based Integrity Evaluation System )

정민중,김영진,표창률 대한기계학회 1999 대한기계학회 춘추학술대회 Vol.- No.-

다차원 설계윈도우 탐색법을 이용한 마이크로 액추에이터 형상설계

정민중,김영진,다이수케이시하라,시노부요시무라,겐기야가와,Jeong, Min-Jung,Kim, Yeong-Jin,Daisuke Ishihara,Yoshimura, Shinobu,Yagawa, Genki 대한기계학회 2001 大韓機械學會論文集A Vol.25 No.11

For micro-machines, very few design methodologies based on optimization hale been developed so far. To overcome the difficulties of design optimization of micro-machines, the search method for multi-dimensional design window (DW)s is proposed. The proposed method is defined as areas of satisfactory design solutions in a design parameter space, using both continuous evolutionary algorithms (CEA) and the modified K-means clustering algorithm . To demonstrate practical performance of the proposed method, it was applied to an optimal shape design of micro electrostatic actuator of optical memory. The shape design problem has 5 design parameters and 5 objective functions, and finally shows 4 specific design shapes and design characters based on the proposed DWs.

유도 결합형 플라즈마에서 In-situ 플라즈마 전자밀도 측정방법 연구

정민중,김곤호 한양대학교 이학기술연구소 2002 이학기술연구지 Vol.5 No.-

유도 결합성 플라즈마 발생 장치에서 플라즈마 밀도를 측정하기 위한 In-Situ 플라즈마 진단 방법을 개발하였다. 안테나로 인가된 전력은 모두 플라즈마를 발생시키는데 소모되었다고 가정하여, 전력 균형식으로부터 안테나에 인가된 전력과 플라즈마 내부인자의 함수관계를 유도하고, 안테나 안가 전력의 전류와 전압을 측정하여 전자밀도를 유추할 수 있다. 안테나의 전류와 전압을 실시간으로 측정하는 전력측정 장치를 제작하고, 아르곤 가스를 이용하여 50, 40 및 30 mtorr의 운전 압력에서 인가 전력을 300- 800W로 바꾸어 가면서 실험하였다. 정전 탐침을 이용해서 반옹기 내부에서 직접 얻은 플라즈마 밀도와 안테나에 인가된 전력을 이용하여 측정된 전자밀도의 비율은 인가 전력에 무관하게 일정한 값을 보였으나, 운전 압력에 따라서 0.1 , 0.3 그리고 0.5의 값을 가졌다. 개발된 진단 방법이 운전 압력에 민감하나 플라즈마 밀도 변화를 정성적으로 관측할 수 있는 방법임을 보였다. In-situ plasma density monitoring system in an inductively coupled plasma source has been developed. Assuming the input power delivered only to the plasma generation, the relation between the delivery Power on the antenna and the plasma parameters can be obtained from the power balance equation. The in-situ system to monitor the current and voltage of the antenna was manufactured. Experiments were carried out under Ar gas pressures, 50, 40, and 30 mTorr with varying the rf power from 300 to 500w, respectively. Plasma parameters were measured directly by the electrical probe and compared to the results taken from the power monitoring system. The comparison shows that the power monitoring system was not sensitive to the input power but to the operating pressure. The system can beused monitor the qualitative behaviour of the plasma in the chamber .

e-사이언스 기반 계산시스템을 이용한 단백질 접힘해석

정민중(Min Joong Jeong),김병상(Byung Sang Kim) 대한기계학회 2006 대한기계학회 춘추학술대회 Vol.2006 No.11

Many engineering problems often require the large amount of computing resources for iterative simulations of problems treating many parameters and input files. In order to overcome the situation, this paper proposes an e-Science based computational system. The system exploits the Grid computing technology to establish an integrated web service environment which supports distributed computational simulations and remote executions. The proposed system provides an easy-to-use parametric study service where a computational service includes real time monitoring. To verify usability of the proposed system, thousands of protein folding simulations were carried out and explored a native-like three dimensional protein structure.

단백질 접힘 시뮬레이션을 위한 최적알고리즘 개발

정민중(Min-Joong Jeong) 대한기계학회 2008 대한기계학회 춘추학술대회 Vol.2008 No.5

Computational modeling of the unique tertiary structure of a protein from its amino acid sequence alone is one of the important challenges in science and technology. The tertiary structure itself and the folding mechanism toward it are indispensable for under-standing the function and biological role of the protein. In this study, a new modeling method to predict protein tertiary structures is proposed. The proposed method mainly consists of global folding optimization to construct protein structures. One of our computational modeling of protein, which was gauged 2.12 A of RMSD on its native tertiary structure, is provided with other experiments.