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A Heuristic Algorithm to Find All Normalized Local Alignments Above Threshold
Kim, Sangtae,Sim, Jeong Seop,Park, Heejin,Park, Kunsoo,Park, Hyunseok,Seo, Jeong-Sun Korea Genome Organization 2003 Genomics & informatics Vol.1 No.1
Local alignment is an important task in molecular biology to see if two sequences contain regions that are similar. The most popular approach to local alignment is the use of dynamic programming due to Smith and Waterman, but the alignment reported by the Smith-Waterman algorithm has some undesirable properties. The recent approach to fix these problems is to use the notion of normalized scores for local alignments by Arslan, Egecioglu and Pevzner. In this paper we consider the problem of finding all local alignments whose normalized scores are above a given threshold, and present a fast heuristic algorithm. Our algorithm is 180-330 times faster than Arslan et al.'s for sequences of length about 120 kbp and about 40-50 times faster for sequences of length about 30 kbp.
Development of a Two-Wheeled Mobile Tilting & Balancing (MTB) Robot
Sangtae Kim,Jungmin Seo,SangJoo Kwon 제어로봇시스템학회 2011 제어로봇시스템학회 국제학술대회 논문집 Vol.2011 No.10
Two wheeled mobile balancing robot is a kind of under-actuation system that can maintain its posture and drive the robot with only two wheels. In order to overcome the limitation in turning velocity due to the centrifugal force effect, this paper proposes a tilting balancing mechanism which is to offset the centrifugal force by active tilting motions. The newly suggested two-wheeled mobile tilting and balancing robot (MTB) can prevent unnecessary slowdowns in turning motions and increase passenger?s riding feelings. To validate the tilting effect, the equation of motion of the MTB robot is derived and analyzed and the hardware design is followed.
Nonlinear Optimal Control Design for Underactuated Two-Wheeled Inverted Pendulum Mobile Platform
Kim, Sangtae,Kwon, SangJoo IEEE 2017 IEEE/ASME transactions on mechatronics Vol.22 No.6
<P>In terms of the state-dependent Riccati equation (SDRE) control framework, a nonlinear motion control is investigated for the two-wheeled inverted pendulum (TWIP) mobile robot platform. As a critical design issue, the state dependent coefficient matrix is established based on the sound understanding of dynamic characteristics of the TWIP robot. The developed SDRE control solution has the merit of robust posture stabilization when the inverted pendulum robot experiences strong nonlinear behaviors due to abrupt external disturbances.</P>
Kim, Sangtae,Park, Heejin,Lee, Kong-Joo,Paek, Eunok 이화여자대학교 세포신호전달연구센터 2006 고사리 세포신호전달 심포지움 Vol. No.8
Identification of post-translational modifications(PTMs) is important to understand cellular functions of proteins. Various computational methods have been developed to interpret MS/MS spectra for PTM identification, but they are applicable only if the number of PTM sites and types being considered are limited. As the number of PTM sites and PTM types increase, the execution time and the space consumption required by the current software algorithms grow exponentially. To identify multiple PTMs in MS/MS spectra, we present here an innovative algorithm called MOD^(i) that makes use of a tag chain, which is a list of sequence tags and in-between gaps. The tag chain method differs from former tag-based techniques in that it uses multiple adjacent and nonadjacent tags to interpret MS/MS spectra while the former techniques use either only one tag or adjacent tags. The proposed method performs well even when more than a hundred modification types are considered and multiple potential PTMs exist in a peptide, as in the case of proteins such as histones and GAPDH. MOD^(i) manages the computational complexity of PTM identification innovatively and therefore can serve as an effective software platform for identifying multiple PTMs.
Error Probability Expressions for Frame Synchronization Using Differential Correlation
Sangtae Kim,Jaewon Kim,신동준,장대익,성원진 한국통신학회 2010 Journal of communications and networks Vol.12 No.6
Probabilistic modeling and analysis of correlation metrics have been receiving considerable interest for a long period of time because they can be used to evaluate the performance of communication receivers, including satellite broadcasting receivers. Although differential correlators have a simple structure and practical importance over channels with severe frequency offsets, closedform expressions for the output distribution of differential correlators do not exist. In this paper, we present detection error probability expressions for frame synchronization using differential correlation,and demonstrate their accuracy over channel parameters of practical interest. The derived formulas are presented in terms of the Marcum Q-function, and do not involve numerical integration,unlike the formulas derived in some previous studies. We first determine the distributions and error probabilities for single-span differential correlation metric, and then extend the result to multispan differential correlation metric with certain approximations. The results can be used for the performance analysis of various detection strategies that utilize the differential correlation structure.
SDRE 기법을 이용한 이륜 밸런싱 로봇의 비선형 최적제어
김상태(Sangtae Kim),권상주(SangJoo Kwon) 제어로봇시스템학회 2011 제어·로봇·시스템학회 논문지 Vol.17 No.10
Two-wheeled balancing mobile robots are currently controlled in terms of linear control methods without considering the nonlinear dynamical characteristics. However, in the high maneuvering situations such as fast turn and abrupt start and stop, such neglected terms become dominant and greatly influence the overall driving performance. This paper addresses the SDRE nonlinear optimal control method to take advantage of the exact nonlinear dynamics of the balancing robot. Simulation results indicate that the SDRE control outperforms LQR in the respect of transient performance and required wheel torques. A design example is suggested for the state matrix that provides design flexibility in the SDRE control. It is shown that a well-planned state matrix by reflecting the physics of a balancing robot greatly contributes to the driving performance and stability.