Medial-ABC: an algorithm for the correspondence between myocardium and coronary artery mesh models based on the medial axis of coronary artery

Jehyun Cha,Joong Hyun Ryu,Jin-Ho Choi,Deok-Soo Kim 한국CDE학회 2020 Journal of computational design and engineering Vol.7 No.6

The role of coronary arteries is to supply sufficient blood to myocardium. Obstruction of coronary arteries limits blood supply and causes myocardial ischemia or acute myocardial infarction, a major cause of human death. Hence, the quantification of the regional amount of heart muscle subtended by obstructed coronary arteries is of critical value in clinical medicine. However, conventional methods are inaccurate and frequently disagree with clinical practice. This study proposes a novel medial-axis-based correspondence (Medial-ABC) algorithm to find the correspondence between myocardium and coronary artery in order to segment regional myocardium at risk subtended by any potentially obstructed coronary artery. Given the triangular mesh models of coronary artery and myocardium, the proposed algorithm (i) computes the medial axis of coronary artery, (ii) finds the correspondence using the medial axis of coronary artery, and (iii) segments the coronary artery and myocardium. The proposed algorithm provides a robust mathematical linkage between myocardium at risk and supplying coronary arteries so that ischemic myocardial regions can be accurately identified. Hence, both the extent and severity of myocardial ischemia can be quantified effectively, efficiently, and accurately. Furthermore, the constructed mesh model of segmented coronary artery and myocardium can be post-processed for applications such as building optimization models of cardiac systems. The CardiacVis program, which implements the Medial-ABC algorithm, is freely available at Voronoi Diagram Research Center (http://voronoi.hanyang.ac.kr/software/cardiacvis) and will be an invaluable tool for quantitative patient-specific risk stratification in clinical practice.

Generation, transport and detection of valley-locked spin photocurrent in WSe2-graphene-Bi2Se3 heterostructures

Cha, Soonyoung,Noh, Minji,Kim, Jehyun,Son, Jangyup,Bae, Hyemin,Lee, Doeon,Kim, Hoil,Lee, Jekwan,Shin, Ho-Seung,Sim, Sangwan,Yang, Seunghoon,Lee, Sooun,Shim, Wooyoung,Lee, Chul-Ho,Jo, Moon-Ho,Kim, Jun Nature Publishing Group 2018 Nature nanotechnology Vol.13 No.10

위상에 기반한 원의 Voronoi diagram 계산

이목원(Mokwon Lee),차제현(Jehyun Cha),송찬영(Chanyoung Song),김재관(Jae-Kwan Kim),조영송(Youngsong Cho),유중현(Joonghyun Ryu),김덕수(Deok-Soo Kim) (사)한국CDE학회 2014 한국 CAD/CAM 학회 학술발표회 논문집 Vol.2014 No.8

Voronoi diagrams are useful for reasoning spatial properties among particles. In particular, the Voronoi diagram of circles in 2D is important on its own and has many applications. And also it is meaningful for extending to that of spheres in 3D. In this paper, we propose a new algorithm for construction of Voronoi diagram of circles. This algorithm constructs the Voronoi diagram by adding a new circle to the already constructed one and then changing the topology influenced by the new circle. The approach using topology uses logical computations instead of numerical computations. That reduces the number of numerical errors.

BetaSCPWeb: side-chain prediction for protein structures using Voronoi diagrams and geometry prioritization

Ryu, Joonghyun,Lee, Mokwon,Cha, Jehyun,Laskowski, Roman A.,Ryu, Seong Eon,Kim, Deok-Soo Oxford University Press 2016 Nucleic acids research Vol.44 No.w1

<P>Many applications, such as protein design, homology modeling, flexible docking, etc. require the prediction of a protein's optimal side-chain conformations from just its amino acid sequence and backbone structure. Side-chain prediction (SCP) is an NP-hard energy minimization problem. Here, we present BetaSCPWeb which efficiently computes a conformation close to optimal using a geometry-prioritization method based on the Voronoi diagram of spherical atoms. Its outputs are visual, textual and PDB file format. The web server is free and open to all users at http://voronoi.hanyang.ac.kr/betascpweb with no login requirement.</P>

CFX를 이용한 축류 터빈의 정상, 비정상 유동 특성 비교

황동하(Dongha Hwang),정요한(Yohan Jung),백제현(Jehyun Baek),차봉준(Bongjun Cha) 한국유체기계학회 2008 유체기계 연구개발 발표회 논문집 Vol.2008 No.-

SqueeView: 공간지각능력 향상을 위한 기능성 게임

최용준(Yong-June Choi),차제현(Jehyun Cha),류호경(Hokyoung Ryu) 한국HCI학회 2012 한국HCI학회 학술대회 Vol.2012 No.1

기능성 게임 산업의 많은 발전이 있었지만, 게임을 통한 실생활 효과는 제대로 평가가 이루어 지지 않고 있다. 본 논문에서는 "SqueeView"라는 새로운 개념의 게임 콘트롤러을 사용하여 기능성 게임을 수행하게 하고, 공간 지각능력 향샹 효과를 통하여 얻어질 수 있는 실생활 적용 효과에 대한 실험을 진행하였다. 이 연구의 결과를 통하여 기능성 게임을 통한 효과를 실증적으로 평가하였고, 이를 통하여 새로운 기능성 게임 평가방법론을 제시한다. With the success and proliferation of video games, there can be no doubt that video games are a part of our culture. Many disciplines (Government agencies, the military, hospital and so forth) at every educational level now use video games as a part of training or education purposes. Yet, it is still arguable whether serious games can present something other than playfulness or enjoyment, and whether the learning experience from serious games would be beyond and above those from other learning tools (e.g., cognitive rehabilitation devices such as Purdue Pegwork). In particular, it can be seen that the learning effect from serious games would not be transferrable to other problem solving situations. The present study aims to address this question, using a novel input device (i.e., SqueeView), whether it can create a critical learning effect in performing normal mundane tasks in real life. The empirical study revealed that the essential learning effect from 'SqueeView' was applicable to many real life tasks, and based on this an evaluative framework for serious games was presented.

MGOS: A library for molecular geometry and its operating system

Kim, Deok-Soo,Ryu, Joonghyun,Cho, Youngsong,Lee, Mokwon,Cha, Jehyun,Song, Chanyoung,Kim, Sang Wha,Laskowski, Roman A.,Sugihara, Kokichi,Bhak, Jong,Ryu, Seong Eon Elsevier 2020 Computer physics communications Vol.251 No.-

<P><B>Abstract</B></P> <P>The geometry of atomic arrangement underpins the structural understanding of molecules in many fields. However, no general framework of mathematical/computational theory for the geometry of atomic arrangement exists. Here we present “Molecular Geometry (MG)” as a theoretical framework accompanied by “MG Operating System (MGOS)” which consists of callable functions implementing the MG theory. MG allows researchers to model complicated molecular structure problems in terms of elementary yet standard notions of volume, area, etc. and MGOS frees them from the hard and tedious task of developing/implementing geometric algorithms so that they can focus more on their primary research issues. MG facilitates simpler modeling of molecular structure problems; MGOS functions can be conveniently embedded in application programs for the efficient and accurate solution of geometric queries involving atomic arrangements. The use of MGOS in problems involving spherical entities is akin to the use of math libraries in general purpose programming languages in science and engineering.</P> <P><B>Program summary</B></P> <P> <I>Program Title:</I> Molecular Geometry Operating System (MGOS)</P> <P> <I>Program Files doi:</I> http://dx.doi.org/10.17632/hp2wmvxsfz.1 </P> <P> <I>Licensing provisions:</I> CC By 4.0</P> <P> <I>Programming language:</I> C++</P> <P> <I>Supplementary material:</I> (1) Supplementary Video 1, (2) Supplementary Video 2, (3) Supplementary Video 3, (4) Supplementary Video 4, (5) MGOS manual, and (6) 300 test PDB structure files</P> <P> <I>Nature of problem:</I> For both organic and inorganic molecules, structure determines molecular function and molecular structure is highly correlated with molecular shape or geometry. Hence, many studies were conducted for the analysis and evaluation of the geometry of atomic arrangement. However, most studies were based on Monte Carlo, grid-counting, or approximation methods and a high-quality solution requires heavy computational resources, not to mention its dependency on computation environment. In this paper, we introduce a unified framework of computational library, Molecular Geometry Operating System (MGOS), based on an analytic method for the molecular geometry of atomic arrangements. We believe that the powerful MGOS application programming interface (API) functions will free scientists from developing and implementing complicated geometric algorithms and let them focus on more important scientific problems.</P> <P> <I>Solution method:</I> Molecular Geometry (MG) is a general framework of mathematical/computational methods for solving molecular structure problems using a geometry-priority philosophy and is implemented by MGOS which is a library of callable C++ API functions. MGOS is developed based on the Voronoi diagram of three-dimensional spheres and its two derivative constructs called the quasi-triangulation and beta-complex. Note that this Voronoi diagram is different from the ordinary Voronoi diagram of points where the points are atom centers. Being an analytic method, the solutions of many geometric queries on atomic arrangement, if not all, are obtained correctly and quickly. The MGOS architecture is carefully designed in a three-tier architecture so that future modifications and/or improvements can be reflected in the application programs with no additional programming by users.</P>

BetaConcpet 프로그램: 2 차원 평면의 Voronoi diagram, 쌍대구조 그리고 콤플렉스

김재관(Jae-Kwan Kim),이목원(Mokwon Lee),차제현(Jehyun Cha),송찬영(Youngsong Song),조영송(Youngsong Cho),유중현(Joonghyun Ryu),김덕수(Deok-Soo Kim) (사)한국CDE학회 2014 한국 CAD/CAM 학회 학술발표회 논문집 Vol.2014 No.8

Voronoi diagrams are powerful for solving spatial problems among particles with different sizes.Voronoi diagram of atoms has proven its power for solving various fields of different disciplines, particularly molecular biology/material science problems, in an unified framework. Beta-complex is a generalization of alpha-complex and they share similarities and dissimilarities. This paper presents the BetaConcept program which facilitates easy understanding of the powerful capability of the Voronoi diagram, its dual structure, and the beta-complex in the plane. BetaConcept is a Windows program with a graphic user interface written in the standard C++ language and is freely available at the Voronoi Diagram Research Center (http://voronoi.hanyang.ac.kr).

프레임 기반 스케줄러를 위한 주기적 패킷 폐기 기법

이성형(Sung-Hyung Lee),이현진(Hyun-Jin Lee),차재룡(Jae-Ryong Cha),김재현(Jae-Hyun Kim),금동원(Dong-Won Kum),백해현(Hae-Hyeon Baek),신상헌(Sang-heon Shin),전제현(Jehyun Jun) 한국통신학회 2013 韓國通信學會論文誌 Vol.38 No.2B

본 논문에서는 프레임 기반 스케줄러에서 지연시간에 민감한 트래픽에 대해 지연시간을 쉽게 제한하기 위한 대기시간 기반 주기적 패킷 폐기 기법에 대해 소개한다. 이 기법은 프레임 기반 스케줄러에서 매 스케줄링 시점에 임계값보다 오래 버퍼에 머물러 있는 패킷을 폐기하는 방법으로 지연시간을 제한한다. 본 논문에서는 제안하는 기법에 대해 혼잡상황에서의 평균 큐잉 지연시간 및 패킷 손실율을 수식적으로 분석하고, 시뮬레이션 결과와 비교하였다. 성능 분석 결과, 제안한 패킷 폐기 기법은 임계값 설정으로 패킷의 큐잉 지연시간을 쉽게 제한할 수 있음을 확인하였다. 또한 패킷 폐기를 스케줄링 이전에 수행함으로 서비스 처리율의 제한이 가능함을 확인하였다. This paper introduces waiting time based periodic packet discard policy for frame based scheduler. This policy can be used with conventional packet discard policy or buffer management schemes, such as drop-tail or random early detection. Proposed discard policy discards packets, which are stayed in the buffer longer than threshold, at every period of scheduling. This decision of discard is based on waiting time of packet. In this paper, mathematical analysis is performed with situation of network congestion. Also, the simulation is performed to evaluate the performance of proposed discard policy. In the result, proposed discard policy can limit queuing delay by threshold. Also, if the packet discard is performed before scheduling and threshold is set with smaller value than frame length, it can limit the throughput of traffic.

BULL! : 분자기하학 엔진

조영송(Youngsong Cho),김재관(Jae-Kwan Kim),유중현(Joonghyun Ryu),이목원(Mokwon Lee),차제현(Jehyun Cha),송찬영(Chanyoung Song),김덕수(Deok-Soo Kim) (사)한국CDE학회 2014 한국 CAD/CAM 학회 학술발표회 논문집 Vol.2014 No.8

Geometric properties are critical for the function of molecules consisting of atoms with different radii which are usually modeled as spheres in 3D. “Molecular Geometry” is a theoretical framework of computational understanding of the geometry of molecules in the claim that most molecular structure problems can be effectively and efficiently facilitated by the “geometrization” of the problem into that among spheres in 3D whose solution can be easily found via “geometry kernel”. In this paper, we report BULL!, the molecular geometry engine based on the Voronoi diagram of spheres, the quasi-triangulation, and the beta-complex. Being a program implemented in C++, application programmers can simply call API-functions of BULL! to create application programs correctly, efficiently, and conveniently. The BULL! is designed compatibly so that application programs are completely independent of future modifications and improvements. The BULL! engine will be freely available from the Voronoi Diagram Research Center at Hanyang University.