Chain molecule deformation in a uniform flow - a computer experiment

MOOKYUNG CHEON,IKSOO CHANG(장익수),JOEL KOPLIK,JAYANTH R. BANAVAR 대한기계학회 2002 대한기계학회 춘추학술대회 Vol.2002 No.4

We investigate the stretching of a polymer in a uniform flow using molecular dynamics (MD) simulations. Our MD simulations represent an ab-initio experiment with no explicit assumption for the dynamics of a single chain except for using the generic Lennard-Jones and the FENE potentials. In spite of the modest length of our simulated chains, the qualitative features of experiments on DNA are reproduced and the predictions of a wormlike chain theory are found to hold, with the polymer molecule being free draining at large extensions.

Identifying Critical Factors for Successful Games by Applying Topic Modeling

Mookyung Kwak,박지수,손진곤 한국정보처리학회 2022 Journal of information processing systems Vol.18 No.1

Games are widely used in many fields, but not all games are successful. Then what makes games successful?The question gave us the motivation of this paper, which is to identify critical factors for successful games withtopic modeling technique. It is supposed that game reviews written by experts sit on abundant insights andtopics of how games succeed. To excavate these insights and topics, latent Dirichlet allocation, a topic modelinganalysis technique, was used. This statistical approach provided words that implicate topics behind them. Fiftytopics were inferred based on these words, and these topics were categorized by stimulation-response-desiregoal(SRDG) model, which makes a streamlined flow of how players engage in video games. This approachcan provide game designers with critical factors for successful games. Furthermore, from this research result,we are going to develop a model for immersive game experiences to explain why some games are moreaddictive than others and how successful gamification works.

서울시 성과참조모델 개발방안

장무경(Mookyung Jang),이지은(Jieun Lee),신신애,이병기,이석준,정국환 서울연구원 2008 서울연구원 정책과제연구보고서 Vol.- No.-

건축에서의 ‘일상성’과 ‘공공성’

김무경(MooKyung Kim) 한국문화사회학회 2014 문화와 사회 Vol.16 No.-

이 논문은 얼마 전 작고하였고, “말하는 건축가”라는 다큐멘터리의 주인공으로도 잘 알려진 건축가 정기용의 ‘무주 프로젝트’와 ‘기적의 도서관’ 연작 등 ‘공공건축물’ 연작을 중심으로 건축에서의 ‘공공성’에 대하여 살펴보는 것을 그 목적으로 한다. 정기용이 구상하는 건축에서의 ‘공공성’은 우선적으로, 주민들이 더 이상 통치의 대상이기 보다는 개별적으로 접근하기 어려운 시설들과 공간의 주인이라는 기본적인 인식에 바탕을 두고, 주민들의 사회관계를 만들고 뿌리내리게 하는 ‘장소’를 만드는 계기로서의 건축을 전제로 한다. 그런데 이와 같은 ‘장소’의 구축에 기본이 되는 것은, 정기용에 의하면, “가장 하찮고 별 볼일 없는 것들, 하지만 반복될 수밖에 없는 것들”인 ‘일상’과 그 “일상이 만드는 문화”이다. 그런데 이 일상은 우리가 여러 차원의 ‘관계’ 속의 존재임을 구체적으로 보여준다. 그 관계는 사람 사이의 관계만이 아니라, 사람과 건축물, 사람과 자연, 자연과 건축물 등 그야말로 ‘전일적’이다. 이로부터 정기용은 ‘감응’의 문제 틀을 강조하게 된다. 그리고 이로부터 또한 왜 정기용이 이 시대의 건축가는 여러 차원의 ‘새로운 관계’를 맺어주는 사람이며, 단지 건물을 지어주는 사람이 아니라 건축설계와 건축프로그램을 동시에 설정해야 하는 ‘사회적 조절자’가 되어야 하고, 왜 현재와 같은 전환기에는 위대한 건축가 보다는 사회적 필요성에 화답하고 보편적 해답을 보다 다수를 위하여 생산해낼 수 있는 ‘사회적 조절자’로서의 보통 건축가가 필요하다고 강조하는 지를 이해하게 된다. This article aims to discuss about the "quotidianty" and the "publicity" in architecture from the series of public architecture of Cheong, Gi-Yong, who had accomplished the "Muju Project" and the "Miracle Library". Cheong, Gi-Yong considers the "publicity" in architecture, above all, as the occasion to establish the "place" which permits to people make the diverse social relations. Nevertheless, what is principal to the construction of this "place", it is, says Cheong, the "quotidian", which, seems at first glance to be negligible. But this "quotidian" shows us concretely that we are beings who are situated always in the "relations" of differents dimensions. Those relations are not only those between men, but also those between men and nature, and those between nature and architecture. Il is this reason why his architecture is called to be "holistic". From this, Cheong emphasizes on the problematic of the "Correspondance". And simultaneously from this, Cheong puts the accent on the role of the architecture as th "social coordinator", especially necessary in the periode of transition and of the new foundation like our time.

유비쿼터스 사회의 정보보호 방안

장무경(Mookyung Jang),최지원(Ji-Won Choi),이지은(Jieun Lee) 서울연구원 2008 서울연구원 정책과제연구보고서 Vol.- No.-

운행자동차의 공회전 정지에 의한 CO₂ 저감량 산출 연구

심무경(Mookyung Shim),임재명(Jay-Myoung Rim),이범호(Beomho Lee),홍성태(Sungtae Hong),이대엽(Daeyup Lee) 대한기계학회 2009 大韓機械學會論文集B Vol.33 No.10

The effect of idling stop on CO₂ reduction was estimated, especially in the area of in-use vehicles. In order to know the fuel saving for each class of vehicles, a methodology to calculate the fuel saving was used along with a standard test using NIER-07 mode. Idling stop execution rate was estimated by analyzing the driving pattern of the in-use city buses, which shows about 75% at maximum. And this corresponds to about 5.4% reduction of the daily total fuel consumption. Finally, CO₂ reduction in the automotive sector was estimated, which concludes that, when idling stop device is used, about 480 thousand and 450 thousand tons of CO₂ could be reduced with in-use city buses and taxis, respectively. This amount corresponds to about 1.2% of CO₂ reduction in the automotive sector.

공회전 정지에 따른 연료 절약 분석 방법의 연구

심무경(Mookyung Shim),임재명(Jay-Myoung Rim),이범호(Beomho Lee),홍성태(Sungtae Hong),이대엽(Daeyup Lee) 한국자동차공학회 2009 한국 자동차공학회논문집 Vol.17 No.6

Uncovering multiloci-ordering by algebraic property of Laplacian matrix and its Fiedler vector

Cheon, Mookyung,Kim, Choongrak,Chang, Iksoo Oxford University Press 2016 Bioinformatics Vol.32 No.6

<P>Motivation: The loci-ordering, based on two-point recombination fractions for a pair of loci, is the most important step in constructing a reliable and fine genetic map. Results: Using the concept from complex graph theory, here we propose a Laplacian ordering approach which uncovers the loci-ordering of multiloci simultaneously. The algebraic property for a Fiedler vector of a Laplacian matrix, constructed from the recombination fraction of the loci-ordering for 26 loci of barley chromosome IV, 846 loci of Arabidopsis thaliana and 1903 loci of Malus domestica, together with the variable threshold uncovers their loci-orders. It offers an alternative yet robust approach for ordering multiloci.</P>

Extending the PRIME model for protein aggregation to all 20 amino acids

Cheon, Mookyung,Chang, Iksoo,Hall, Carol K. Wiley Subscription Services, Inc., A Wiley Company 2010 Proteins Vol.78 No.14

<P><B>Abstract</B></P><P>We extend PRIME, an intermediate‐resolution protein model previously used in simulations of the aggregation of polyalanine and polyglutamine, to the description of the geometry and energetics of peptides containing all 20 amino acid residues. The 20 amino acid side chains are classified into 14 groups according to their hydrophobicity, polarity, size, charge, and potential for side chain hydrogen bonding. The parameters for extended PRIME, called PRIME 20, include hydrogen‐bonding energies, side chain interaction range and energy, and excluded volume. The parameters are obtained by applying a perceptron‐learning algorithm and a modified stochastic learning algorithm that optimizes the energy gap between 711 known native states from the PDB and decoy structures generated by gapless threading. The number of independent pair interaction parameters is chosen to be small enough to be physically meaningful yet large enough to give reasonably accurate results in discriminating decoys from native structures. The most physically meaningful results are obtained with 19 energy parameters. Proteins 2010. © 2010 Wiley‐Liss, Inc.</P>

Structural Conversion of Aβ _17–42 Peptides from Disordered Oligomers to U-Shape Protofilaments via Multiple Kinetic Pathways

Cheon, Mookyung,Hall, Carol K.,Chang, Iksoo Public Library of Science 2015 PLoS computational biology Vol.11 No.5

<▼1><P>Discovering the mechanisms by which proteins aggregate into fibrils is an essential first step in understanding the molecular level processes underlying neurodegenerative diseases such as Alzheimer’s and Parkinson's. The goal of this work is to provide insights into the structural changes that characterize the kinetic pathways by which amyloid-β peptides convert from monomers to oligomers to fibrils. By applying discontinuous molecular dynamics simulations to PRIME20, a force field designed to capture the chemical and physical aspects of protein aggregation, we have been able to trace out the entire aggregation process for a system containing 8 Aβ17–42 peptides. We uncovered two fibrillization mechanisms that govern the structural conversion of Aβ17–42 peptides from disordered oligomers into protofilaments. The first mechanism is monomeric conversion templated by a U-shape oligomeric nucleus into U-shape protofilament. The second mechanism involves a long-lived and on-pathway metastable oligomer with S-shape chains, having a C-terminal turn, en route to the final U-shape protofilament. Oligomers with this C-terminal turn have been regarded in recent experiments as a major contributing element to cell toxicity in Alzheimer’s disease. The internal structures of the U-shape protofilaments from our PRIME20/DMD simulation agree well with those from solid state NMR experiments. The approach presented here offers a simple molecular-level framework to describe protein aggregation in general and to visualize the kinetic evolution of a putative toxic element in Alzheimer’s disease in particular.</P></▼1><▼2><P><B>Author Summary</B></P><P>Understanding the mechanisms of protein folding and aggregation is of fundamental importance in elucidating the biological function of proteins and their complex. Many advances have been made in our ability to describe protein folding based both on ideas from biophysics and improvements in supercomputing power, yet realistic simulations of the entire kinetic process of protein aggregation including fibril formation still remain challenging tasks in biophysics and computational biology. This work describes a breakthrough in our ability to simulate the aggregation of proteins on a molecular level and the emergence of the toxic species responsible for the cause of neuro-degenerative diseases such as Alzheimer’s disease. Based on this work, one can now trace the entire aggregation process starting from disordered monomers to meta-stable oligomers to protofilament and then amyloid fibril. This is a significant advance over the current state of the art in both biophysics and computational biology in uncovering the fundamental mechanisms behind the amyloid fibril formation for aggregation-prone proteins.</P></▼2>