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KOSMOS: a universal morph server for nucleic acids, proteins and their complexes
Seo, Sangjae,Kim, Moon Ki Oxford University Press 2012 Nucleic acids research Vol.40 No.w1
<P>KOSMOS is the first online morph server to be able to address the structural dynamics of DNA/RNA, proteins and even their complexes, such as ribosomes. The key functions of KOSMOS are the harmonic and anharmonic analyses of macromolecules. In the harmonic analysis, normal mode analysis (NMA) based on an elastic network model (ENM) is performed, yielding vibrational modes and B-factor calculations, which provide insight into the potential biological functions of macromolecules based on their structural features. Anharmonic analysis involving elastic network interpolation (ENI) is used to generate plausible transition pathways between two given conformations by optimizing a topology-oriented cost function that guarantees a smooth transition without steric clashes. The quality of the computed pathways is evaluated based on their various facets, including topology, energy cost and compatibility with the NMA results. There are also two unique features of KOSMOS that distinguish it from other morph servers: (i) the versatility in the coarse-graining methods and (ii) the various connection rules in the ENM. The models enable us to analyze macromolecular dynamics with the maximum degrees of freedom by combining a variety of ENMs from full-atom to coarse-grained, backbone and hybrid models with one connection rule, such as distance-cutoff, number-cutoff or chemical-cutoff. KOSMOS is available at http://bioengineering.skku.ac.kr/kosmos.</P>
서상재(Sangjae Seo),김문기(Moon Ki Kim) 한국정보기술학회 2010 한국정보기술학회논문지 Vol.8 No.12
In this paper, we propose a needle insertion simulator based on a haptic device with which medical doctors can practice lumbar puncture and epidural anesthesia. This training simulator is composed of 6 DOF Phantom Desktop Haptic hardware and software, which enables us to provide both visual and force feedbacks for better realism. Human anatomical data were acquired from other references and used for developing the skin deformation algorithm to maximize the reality. Through this study, we could retrieve the similar force profile as real force profile shows, using haptic device. It is expected that this research cannot only assist virtual epidural injection training but also improve the needle biopsy technique.
차분 전력 분석 공격을 위한 향상되고 실제적인 신호 정렬 방법
박제훈(JeaHoon Park),문상재(SangJae Moon),하재철(JaeCheol Ha),이훈재(HoonJae Lee) 한국정보보호학회 2008 정보보호학회논문지 Vol.18 No.5
스마트카드, USB token과 같은 저 전력 정보보호장치의 가장 큰 위협요소인 부채널 공격은 장치 내부에 구현된 암호 알고리즘의 이론적인 안전도와는 무관하게 적용될 수 있다. 특히, 부채널 공격들 중에서 차분 전력분석 공격은 적용이 쉽고 근본적인 방어가 어려워서 매우 위협적인 공격이지만 공격을 적용하기 위해서는 측정된 모든 신호가 시간축 상에서 매우 잘 정렬된 신호라는 전제조건이 필요하기 때문에, 트리거 지터링, 잡음, 차분 전력 분석 공격 방어책 등 여러 요인들에 의해 시간축 상에 정렬되지 않은 측정된 신호를 정렬하기 위한 여러 가지 방법들이 제안되어 왔다. 기존의 신호 정렬방법들은 측정된 신호의 시간축 상의 위치만을 정렬하는 방법들이어서, 랜덤 클럭을 이용하여 알고리즘의 수행 시간(시간축 상의 신호 크기)을 변화시키는 차분 전력 분석 대응 방법에는 적용이 되지 않는다. 본 논문에서는 측정된 소비 전력 신호를 보간(interpolation)과 추출(decimation) 과정을 통해서 시간축 상에서 위치뿐만 아니라 크기도 동시에 정렬시키는 향상된 신호 정렬 방법을 제안하였다. 또한 랜덤 클럭 방식의 차분 전력 분석 공격 방어대책이 구현된 스마트카드 칩에 개선된 신호 정렬 방법을 적용하여 차분 전력 분석 공격이 효과적으로 적용됨을 실험적으로 확인하였다. Side channel attacks are well known as one of the most powerful physical attacks against low-power cryptographic devices and do not take into account of the target's theoretical security. As an important succeeding factor in side channel attacks (specifically in DPAs), exact time-axis alignment methods are used to overcome misalignments caused by trigger jittering, noise and even some countermeasures intentionally applied to defend against side channel attacks such as random clock generation. However, the currently existing alignment methods consider only on the position of signals on time-axis, which is ineffective for certain countermeasures based on time-axis misalignments. This paper proposes a new signal alignment method based on interpolation and decimation techniques. Our proposal can align the size as well as the signals’ position on time-axis. The validity of our proposed method is then evaluated experimentally with a smart card chip, and the results demonstrated that the proposed method is more efficient than the existing alignment methods.
DNA nanotube formation based on normal mode analysis
Qian, PengFei,Seo, Sangjae,Kim, Junghoon,Kim, Seungjae,Lim, Byeong Soo,Liu, Wing Kam,Kim, Bum Joon,LaBean, Thomas Henry,Park, Sung Ha,Kim, Moon Ki IOP Pub 2012 Nanotechnology Vol.23 No.10
<P>Ever since its inception, a popular DNA motif called the cross tile has been recognized to self-assemble into addressable 2D templates consisting of periodic square cavities. Although this may be conceptually correct, in reality certain types of cross tiles can only form planar lattices if adjacent tiles are designed to bind in a corrugated manner, in the absence of which they roll up to form 3D nanotube structures. Here we present a theoretical study on why uncorrugated cross tiles self-assemble into counterintuitive 3D nanotube structures and not planar 2D lattices. Coarse-grained normal mode analysis of single and multiple cross tiles within the elastic network model was carried out to expound the vibration modes of the systems. While both single and multiple cross tile simulations produce results conducive to tube formations, the dominant modes of a unit of four cross tiles (one square cavity), termed a quadruplet, fully reflect the symmetries of the actual nanotubes found in experiments and firmly endorse circularization of an array of cross tiles.</P>
Lim, Jang Gyun,Seo, Sangjae,Koo, Jae Mean,Seok, Chang Sung,Choi, Jae Boong,Kim, Moon Ki Elsevier Sequoia 2017 Surface & coatings technology Vol.315 No.-
<P><B>Abstract</B></P> <P>The use of thermal barrier coatings (TBCs) is expected to become more popular in various gas turbines because these coatings provide excellent thermal insulation and damage protection. However, unexpectedly early failure has often discouraged the full use of TBC, resulting in a shortening of the life span of gas turbines because these substrates are directly exposed to harsh operation conditions. The general mechanics of TBC and its complex inner phenomena, mainly related to failure, have been investigated to prolong the lifetime of TBC. However, our understanding is limited because TBC has various specifications and operating conditions, and complex interplays between many factors. The primary goal of this study is to construct an extensive finite element method (FEM) model to evaluate thermal stress of an air plasma sprayed TBC under its operating conditions by considering various inner phenomena, including thermal grown oxide, undulating topology of coating interface, aluminum depletion, creep effect, and elastoplastic deformation. With the proposed FEM model, a parametric study has been conducted with respect to a variety of material properties, as well as the thickness of bond coat and of top coat. The influence of each design factor on thermal stress and the other parameters is fully discussed. Finally, this work leads to optimal design criteria for minimizing thermal stress across a wide range of TBC systems.</P> <P><B>Highlights</B></P> <P> <UL> <LI> A parametric study was carried out for optimal design of thermal barrier coating. </LI> <LI> Elastic modulus of top coat is the most sensitive design parameter to thermal stress. </LI> <LI> Thermal expansion mismatch between top and bond coat was tuned by coating thickness. </LI> </UL> </P>