Improving physical realism, stereochemistry, and side‐chain accuracy in homology modeling: Four approaches that performed well in CASP8

Krieger, Elmar,Joo, Keehyoung,Lee, Jinwoo,Lee, Jooyoung,Raman, Srivatsan,Thompson, James,Tyka, Mike,Baker, David,Karplus, Kevin Wiley Subscription Services, Inc., A Wiley Company 2009 Proteins Vol.77 No.suppl9

<P>A correct alignment is an essential requirement in homology modeling. Yet in order to bridge the structural gap between template and target, which may not only involve loop rearrangements, but also shifts of secondary structure elements and repacking of core residues, high-resolution refinement methods with full atomic details are needed. Here, we describe four approaches that address this 'last mile of the protein folding problem' and have performed well during CASP8, yielding physically realistic models: YASARA, which runs molecular dynamics simulations of models in explicit solvent, using a new partly knowledge-based all atom force field derived from Amber, whose parameters have been optimized to minimize the damage done to protein crystal structures. The LEE-SERVER, which makes extensive use of conformational space annealing to create alignments, to help Modeller build physically realistic models while satisfying input restraints from templates and CHARMM stereochemistry, and to remodel the side-chains. ROSETTA, whose high resolution refinement protocol combines a physically realistic all atom force field with Monte Carlo minimization to allow the large conformational space to be sampled quickly. And finally UNDERTAKER, which creates a pool of candidate models from various templates and then optimizes them with an adaptive genetic algorithm, using a primarily empirical cost function that does not include bond angle, bond length, or other physics-like terms.</P>

Bimodal colloid gels of highly size-asymmetric particles.

Lee, Jooyoung,Lee, Seong Jae,Ahn, Kyung Hyun,Lee, Seung Jong Published by the American Physical Society through 2015 Physical review. E, Statistical, nonlinear, and so Vol.92 No.1

<P>We report a type of colloidal gel, induced by a minute incremental addition of mutually attractive small particles (size ???12 nm) to a suspension of highly charged large particles (size ???500 nm). The gel's morphological behavior does not follow the typical power-law scaling for fractal clusters. Its unique scaling behavior has two distinct power-law indices, based on particle volume fraction. We show the unique scaling behavior arises when nonfractal networks of large particles are bridged by small-particle clusters, which occurs between a lower and upper critical boundary of small particle volume fraction.</P>

한국 중세 서사시의 서사 구성 방식과 장르적 특질

이주영(Lee Jooyoung) 서강대학교 인문과학연구소 2012 서강인문논총 Vol.0 No.33

고려 중후기와 조선 초기의 서사시와 관련된 장르 논의는 아직 합의된 결론에 이르지 못했다. 특히 조선 초의 『용비어천가』는 서사시라 말해지기도 하고 악장(樂章)으로 분류되기도 한다. 서사시로의 규정 역시 에피소드식 구성으로 인해 교술시라는 주장이 있었다. 그럼에도 불구하고 본고에서 다룬 4편의 작품에 관해 논할 때 서사시적 성격을 언제나 언급하는 것도 사실이다. 따라서 이 글에서는 고려 중후기 이규보의 『동명왕편(東明王篇)』, 이승휴의 『제왕운기(帝王韻紀)』, 조선 초기의 『용비어천가(龍飛御天歌)』, 『월인천강지곡(月印千江之曲)』 4편의 작품을 서사시로 느끼게 하는 것이 무엇인지 살펴보는 데 초점을 맞추면서 동시에 서사시의 장르적 성격에 대해서도 살피려는 데 목적을 두었다. 그 결과 4편의 작품들은 모두 집단적 보편성을 가진 세계관을 갖고 있으면서도 서사 구성 방식에 있어서는 유기적인 플롯과 에피소드로 나누어짐을 확인했다. 이런 구성 방식은 차이는 주제의 보편성을 전제하는가, 보편성을 추구하는가의 차이에서 비롯된 것이었다. 보편성이 전제될 경우 유기적 플롯을 통해 주제를 집약해 강조하여 보여주는 형태를 가졌다. 반대로 보편성을 추구할 경우 그 주제를 폭넓은 사건을 통해 입증하려는 형태를 취했다. 하지만 그것은 시적 화자의 시점이 집단적 보편성 위에 기초하고 있다는 걸 말해준다. 나아가 보편적 세계관 아래 이 시적 화자의 시점은 독자의 시점, 그리고 제시된 사건인 객관적 상관물과도 동질성을 가진다. 그로 인해 시적 화자와 객관적 상관물 사이의 동질성 지향은 서정적 성격을, 시적 화자와 독자 시점의 동질성 지향은 교술적 성격을 갖게 했다. The genre discussion which relates with an epic poem of the middle and the latter period of the Goryeo and the early Joseon does not reach an agreed conclusion. Especially 『Yongbieocheon-ga(龍飛御天歌)』 of the early Joseon was called as epic poem and classified as Ak-Jang(樂章). There was assertion which is depiction poem by episode composition. Despite when discussing about Lee Gyu-Bo’s 『King Dongmyeong(東明王篇)』, Lee Sung-Hew’s 『Ghewangungi(帝王韻記)』, 『Yongbieocheon-ga(龍飛御天歌)』 and 『Wolinchonkangchikok(月印千江之曲)』 which it will treat from this dissertation to, the epic poem character is frequently referred. So, from this dissertation, it adjusts the focus the element which does to make these works feel with epic poem is what, simultaneously put a objective in even about genre character of epic poem. When it sees the result, 4 works had the view of the world which has all group universality, and the narrative composition method was coming to divide with organic composition and episode. This difference of composition method originated with difference which the universality of subject is prerequisite, or it pursues the universality of subject. The case where the universality is prerequisite had the form which emphasize a subject by integrating. In opposition, the case which pursue a universality had the form which proof the subject by various events. The fact show that a visual point of poetic speaker exists above group universality. Further from lower part of universal view of the world, this visual point of poetic speaker has homogeneity with the point of view of the reader and the objective correlatives-events which are presented. With the result, homogeneous intention of poetic speaker and objective correlatives make lyric character, homogeneous intention of poetic speaker and the point of view of the reader make character of depiction.

Enzyme free cell detachment using pH-responsive poly(amino ester) for tissue regeneration

Tae-Jin Lee,Tepeng Wu,Jung Hwan Park,Jihun Song,Gun-Jae Jeong,Jiyu Hyun,Jooyoung Lee,Soo-Hong Lee,Doo Sung Lee,Suk Ho Bhang 한국공업화학회 2020 Journal of Industrial and Engineering Chemistry Vol.88 No.-

Despite the advantages of stem cell injection to the skin wound site, this technique is limited in terms ofthe delivery of therapeutically functional stem cells to the wound site. Considering the abnormalmicroenvironment of a wound site, even a small damage or loss of cell function induced by severe trypsintreatment might lead to decrement of the therapeutic efficacy of stem cells. In this study, we havesynthesized pH-responsive polymer mixed poly(amino ester) (mPAE), which can provide the appropriatecell culture condition for cell growth without cytotoxicity along with the maintenance of extracellularmatrix after detachment using low pH (6.0) PBS. Human adipose derive stem cells (hADSCs) cultured onand detached from mPAE-coated tissue culture plates (TCPs) showed similar cell adhesion andangiogenic paracrine factor secretion, compared to hADSCs cultured on and detached from TCPs withtrypsin. As a result, hADSCs detached with pH 6.0 PBS from mPAE-coated TCPs showed similartherapeutic angiogenesis and wound regeneration, compared to the hADSCs detached with trypsin fromTCPs. In conclusion, our pH-responsive polymer, mPAE, might be utilized as an enzyme-free celldetachment system for future tissue engineering.

A Nonlinear Programming for Allocating the Gas Facilities in order to Minimize Domino Effect

JooYoung Lee(이주영),JoongWon Lee(이중원),EnSup Yoon(윤인섭) 한국가스학회 2005 한국가스학회 학술대회논문집 Vol.2005 No.5

Multiple Polypoid Angiodysplasia with Obscure Overt Bleeding

Jooyoung Lee,Sung Wook Hwang,Jihye Kim,Jinwoo Kang,Gyeong Hoon Kang,Kyu-Joo Park,Jong Pil Im,Joo Sung Kim 대한소화기내시경학회 2016 Clinical Endoscopy Vol.49 No.1

Angiodysplasia (AD) is increasingly being recognized as a major cause of gastrointestinal bleeding. Morphologically flat lesions are common types of AD, whereas the polypoid types are rare. We report a case of multiple polypoid AD in the small bowel causing severe anemia and requiring surgical treatment. A 60-year-old male patient visited our hospital with dyspnea and hematochezia. He had a history of myocardial infarction and was taking both aspirin and clopidogrel. Capsule endoscopy, enteroscopy, computed tomography, and angiography revealed multifocal vascular lesions with a polypoid shape in the jejunum. Surgical resection was performed because endoscopic treatment was considered impossible with the number and the location of lesions. The risk of recurrent bleeding related to the use of antiplatelet agents also contributed to the decision to perform surgery. AD was histologically diagnosed from the surgical specimen. He resumed taking both aspirin and clopidogrel after surgery. He fully recovered and has been doing well during the several months of follow-up.

Nickel–copper hybrid electrodes self-adhered onto a silicon wafer by supersonic cold-spray

Lee, Jong-Gun,Kim, Do-Yeon,Kang, Byungjun,Kim, Donghwan,Song, Hee-eun,Kim, Jooyoung,Jung, Woonsuk,Lee, Dukhaeng,Al-Deyab, Salem S.,James, Scott C.,Yoon, Sam S. Elsevier 2015 Acta materialia Vol.93 No.-

<P><B>Abstract</B></P> <P>High-performance electrodes are fabricated through supersonic spraying of nickel and copper particles. These electrodes yield low specific resistivities, comparable to electrodes produced by screen-printed silver paste and light-induced plating. The appeal of this fabrication method is the low cost of copper and large area scalability of supersonic spray-coating techniques. The copper and nickel electrode was fabricated in the open air without any pre- or post-treatment. The spray-coated copper–nickel electrode was characterized by optical microscopy, scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray diffraction, and energy dispersive spectroscopy. Although both SEM and TEM images confirmed voids trapped between flattened particles in the fabricated electrode, this electrode’s resistivity was order 10<SUP>−6</SUP> Ωcm, which is comparable to the bulk value for pure copper.</P> <P><B>Graphical abstract</B></P> <P>[DISPLAY OMISSION]</P>

Hardware design and control method for controlling an input clock frequency in the application

Lee, Kwanho,Lee, Jooyoung The International Promotion Agency of Culture Tech 2016 International Journal of Advanced Culture Technolo Vol.4 No.4

In this paper, the method of controlling the clock that is inputted on the hardware from the application, and the hardware design method are to be proposed. When the hardware is synthesized to the Field Programmable Gate Array(FPGA), the input clock is fixed, and when the input clock is changed, the synthesis process must be passed again to require more time. To solve this problem, the Mixed-Mode Clock Manager(MMCM) module is mounted to control the MMCM module from the application. The controlled MMCM module controls the input clock of the module. The experiment was process the Neural Network algorithm in the x86 CPU and SIMT based processor mounted the FPGA. The results of the experiment, SIMT-based processors, the time that is processed at a frequency of 50MHz was 77ms, 100MHz was 34ms. There was no additional synthesis time due to a change of the clock frequency.

Changes in Direct Healthcare Costs before and after the Diagnosis of Inflammatory Bowel Disease: A Nationwide Population-Based Study

Jooyoung Lee,Jong Pil Im,Kyungdo Han,Jihye Kim,Hyun Jung Lee,Jaeyoung Chun,Joo Sung Kim 거트앤리버 소화기연관학회협의회 2020 Gut and Liver Vol.14 No.1

Background/Aims: We aimed to investigate the differences in direct healthcare costs between patients with and without inflammatory bowel disease (IBD) and changes in direct healthcare costs before and after IBD diagnosis. Methods: This population-based study identified 34,167 patients with IBD (11,014 patients with Crohn’s disease and 23,153 patients with ulcerative colitis) and 102,501 age-and sex-matched subjects without IBD (the control group) from the National Health Insurance database using the International Classification of Disease, 10th revision codes and the rare intractable disease registration program codes. The mean healthcare costs per patient were analyzed for 3 years before and after IBD diagnosis, with follow-up data available until 2015. Results: Total direct healthcare costs increased and peaked at $2,396 during the first year after IBD diagnosis, but subsequently dropped sharply to $1,478 during the second year after diagnosis. Total healthcare costs were higher for the IBD patients than for the control group, even in the third year before the diagnosis ($497 vs $402, p<0.001). The costs for biologics for the treatment of IBD increased steeply over time, rising from $720.8 in the first year after diagnosis to $1,249.6 in the third year after diagnosis (p<0.001). Conclusions: IBD patients incurred the highest direct healthcare costs during the first year after diagnosis. IBD patients had higher costs than the control group even before diagnosis. The cost of biologics increased steeply over time, and it can be assumed that biologics could be the main driver of costs during the early period after IBD diagnosis.

The Security of Tandem-DM in the Ideal Cipher Model

Lee, Jooyoung,Stam, Martijn,Steinberger, John Springer International 2017 Journal of cryptology Vol. No.

<P>We prove that Tandem-DM, one of the two 'classical' schemes for turning an n-bit blockcipher of 2n-bit key into a double-block-length hash function, has birthday-type collision resistance in the ideal cipher model. For , an adversary must make at least blockcipher queries to achieve chance 0.5 of finding a collision. A collision resistance analysis for Tandem-DM achieving a similar birthday-type bound was already proposed by Fleischmann, Gorski and Lucks at FSE 2009. As we detail, however, the latter analysis is wrong, thus leaving the collision resistance of Tandem-DM as an open problem until now. Our analysis exhibits a novel feature in that we introduce a trick never used before in ideal cipher proofs. We also give an improved bound on the preimage security of Tandem-DM. For , we show that an adversary must make at least blockcipher queries to achieve chance 0.5 of inverting a randomly chosen point in the range. Asymptotically, Tandem-DM is proved to be preimage resistant up to blockcipher queries. This bound improves upon the previous best bound of queries and is optimal (ignoring log factors) since Tandem-DM has range of size .</P>