• The Journal of Korean Association of Computer Education
• /
• v.9 no.4
• /
• pp.63-74
• /
• 2006

A molecular docking is thc process of reducing an unmanageable number of compounds to a limited number of compounds for the target of interest by means of computational simulation. And it is one of a large scale scientific application that requires large computing power and data storage capability. Previous applications or software for molecular docking were developed to be run on a supercomputer, a workstation, or a cluster computer. However the virtual screening using a supercomputer has a problem that a supercomputer is very expensive and the virtual screening using a workstation or a cluster-computer requires a long execution time. Thus we propose Grid service based molecular docking application. We designed a resource broker and a data broker for supporting efficient molecular docking service and developed various services for molecular docking.

• ALGAE
• /
• v.33 no.1
• /
• pp.37-48
• /
• 2018

Alaria is the second largest genus of the Laminariales, which is distributed far into the northern Pacific and Atlantic oceans. Due to its high morphological plasticity, over 100 specific and sub-specific names have been used in Alaria, this has been tailored down to the present 17 species through morphological revision and molecular phylogenetic analysis. Endemic species of Alaria from Russian Far East have not been thoroughly revised since their original description, and few of them were confirmed using molecular data until recently. We carried out morphological and molecular studies on A. paradisea which is an endemic species distributed on the Kurile Islands, first described by Miyabe and Nagai in 1932 as Pleuropterum paradiseum. The range of morphological variability and its distribution was re-evaluated using the type specimen as well as other specimens. Analyses of partial mitochondrial cytochrome c oxidase subunit 1 and nuclear-encoded internal transcribed spacer sequences showed that A. paradisea nested within the genus Alaria, but differs morphologically from any other Alaria species in having additional sporophylls with a central midrib (${\beta}-sporophylls$). Our results showed that A. paradisea clearly belongs to the genus Alaria based on DNA data, although the key morphological character that was used to include this species to the genus Pleuropterum, ${\beta}-sporophylls$, is stable and distinguishes it from other Alaria species.

• The Bulletin of The Korean Astronomical Society
• /
• v.42 no.2
• /
• pp.75.1-75.1
• /
• 2017

Ram pressure due to the intracluster medium (ICM) is known to play a crucial role in removing the cool gas content of a galaxy on a short timescale, potentially driving a star forming galaxy to evolve into a red passive population. Although many HI imaging studies find clear evidence of diffuse atomic gas stripping from cluster galaxies, it is still debatable whether the ram pressure can also strip dense molecular gas. NGC 4522, a Virgo spiral, undergoing strong ram pressure stripping, is one of the few cases where extraplanar CO emission together with stripped HI gas and $H{\alpha}$ knots has been identified, providing an ideal laboratory to study the molecular gas stripping event and the extraplanar star formation activity. The aim of this work is to investigate the origin of extraplanar molecular clouds near NGC 4522 (e.g. stripped or forming in situ), and to probe a relation between the molecular gas surface density and the star formation rate (i.e. the Kennicutt-Schmidt law) at sub-kpc scale, especially in the extraplanar space, using ALMA Cycle 3 CO data and $H{\alpha}$ data of NGC 4522. We present the results from our ALMA observations, and discuss possible scenarios for the origin of extraplanar molecular clouds and to characterize the star formation activity associated with stripped gas outside the galactic disk.

• BMB Reports
• /
• v.42 no.6
• /
• pp.367-372
• /
• 2009

In this study, we showed that WAX9D, a nonspecific lipid-transfer protein found in broccoli, binds palmitate (C16) and stearate (C18) with dissociation constants of 0.56 ${\mu}M$ and 0.52 ${\mu}M$, respectively. WAX9D was fused to thioredoxin protein by genetic manipulation to enhance its solubility. The data revealed strong interaction of Trx-WAX9D with palmitate and stearate. The dissociation constants of Trx-WAX9D for palmitate and stearate were 1.1 ${\mu}M$ and 6.4 ${\mu}M$, respectively. The calculated number of binding sites for palmitate and stearate was 2.5 to 2.7, indicating that Trx-WAX9D can bind three molecules of fatty acids. Additionally, Trx-WAX9D was shown to inhibit the apoptotic effect of palmitate in endothelial cells. Our data using Trx-WAX9D provide insight into the broad spectrum of its biological applications with specific palmitate binding.

• The Bulletin of The Korean Astronomical Society
• /
• v.44 no.1
• /
• pp.71.1-71.1
• /
• 2019

We report the first high-resolution (sub-arcminute) large-scale mapping $^{12}CO$ and $^{13}CO$ observations of the molecular clouds associated with the giant outer Galaxy H II region CTB 102 (KR 1). These observations were made using a newly commissioned receiver on the 13.7-m radio telescope at the Taeduk Radio astronomy Observatory (TRAO). Our observations show that the molecular clouds have a spatial extent of $60{\times}35pc$ and a total mass of $10^{4.8}-10^{5.0}$ solar mass, Infrared data from WISE and 2MASS were used to identify and classify the YSO population associated with ongoing star formation activity within the molecular clouds. Moving away from the H II region, there is an age/class gradient consistent with sequential star formation. The infrared and molecular line data were combined to estimate the star formation efficiency (SFE) of the entire cloud as well as the SFE for various sub regions of the cloud.

• The Bulletin of The Korean Astronomical Society
• /
• v.44 no.1
• /
• pp.69.3-69.3
• /
• 2019

The CHIMPS2 survey is to extend the JCMT HARP $^{13}CO/C^{18}O$ J=3-2 Inner Milky-Way Plane Survey (CHIMPS) and the ${12}^CO$ J=3-2 survey (COHRS) into the inner Galactic Plane, the Central Molecular Zone (CMZ), and a section of the Outer Plane. When combined with the complementary $^{12}CO/^{13}CO/C^{18}O$ J=1-0 survey at the Nobeyama 45m (FUGIN) at matching 15" resolution and sensitivity, and other current CO surveys, the results will provide a complete set of transition data with which to calculate accurate column densities, gas temperatures and turbulent Mach numbers. These will be used to: analyze molecular cloud properties across a range of Galactic environments; map the star-formation efficiency (SFE) and dense-gas mass fraction (DGMF) in molecular gas as a function of position in the Galaxy and its relation to the nature of the turbulence within molecular clouds; determine Galactic structure as traced by molecular gas and star formation; constrain cloud-formation models; study the relationship of filaments to star formation; test current models of the gas kinematics and stability in the Galactic center region and the flow of gas from the disc. It will also provide an invaluable legacy data set for JCMT that will not be superseded for several decades. In this poster, we will present the current status of the CHIMPS2.

• The Bulletin of The Korean Astronomical Society
• /
• v.44 no.2
• /
• pp.39.3-39.3
• /
• 2019

Ram pressure stripping due to the intracluster medium (ICM) is an important environmental process, which causes star formation quenching by effectively removing cold interstellar gas from galaxies in dense environments. The evidence of diffuse atomic gas stripping has been reported in several HI imaging studies. However, it is still under debate whether molecular gas (i.e., a more direct ingredient for star formation) can be also affected and/or stripped by ram pressure. The goal of this thesis is to understand the impact of ram pressure on the molecular gas content of cluster galaxies and hence star formation activity. To achieve this, we conducted a series of detailed studies on the molecular gas properties of three Virgo spiral galaxies with clear signs of active HI gas stripping (NGC 4330, NGC 4402, and NGC 4522) based on high-resolution CO data obtained from the Submillimeter Array (SMA) and Atacama Large Millimeter/submillimeter Array (ALMA). As a result, we find the evidence that the molecular gas disk also gets affected by ram pressure in similar ways as HI even well inside of the stellar disk. In addition, we detected extraplanar 13CO clumps in one of the sample, which is the first case ever reported in ram pressure stripped galaxies. By analyzing multi-wavelength data (e.g., Hα, UV, HI, and CO), we discuss detailed processes of how ram pressure affects star formation activities and hence evolution of cluster galaxies. We also discuss the origin of extraplanar 13CO, and how ram pressure can potentially contribute to the chemical evolution of the ICM.

• Genomics & Informatics
• /
• v.16 no.4
• /
• pp.29.1-29.5
• /
• 2018

Hybrid capture-based targeted sequencing is being used increasingly for genomic variant profiling in tumor patients. Unique molecular index (UMI) technology has recently been developed and helps to increase the accuracy of variant calling by minimizing polymerase chain reaction biases and sequencing errors. However, UMI-adopted targeted sequencing data analysis is slightly different from the methods for other types of omics data, and its pipeline for variant calling is still being optimized in various study groups for their own purposes. Due to this provincial usage of tools, our group built an analysis pipeline for global application to many studies of targeted sequencing generated with different methods. First, we generated hybrid capture-based data using genomic DNA extracted from tumor tissues of colorectal cancer patients. Sequencing libraries were prepared and pooled together, and an 8-plexed capture library was processed to the enrichment step before 150-bp paired-end sequencing with Illumina HiSeq series. For the analysis, we evaluated several published tools. We focused mainly on the compatibility of the input and output of each tool. Finally, our laboratory built an analysis pipeline specialized for UMI-adopted data. Through this pipeline, we were able to estimate even on-target rates and filtered consensus reads for more accurate variant calling. These results suggest the potential of our analysis pipeline in the precise examination of the quality and efficiency of conducted experiments.

• Bulletin of the Korean Chemical Society
• /
• v.32 no.7
• /
• pp.2237-2242
• /
• 2011

Anomalous scaling behaviors such as significantly large growth exponent (${\beta}$) and small reciprocal of dynamic exponent (1/z) values for many molecular crystalline thin films have been reported. In this study, the variation of scaling exponent values and consequent growth behaviors of molecular thin films were more quantitatively analysed using a (1+1)-dimensional surface lateral diffusion model. From these simulations, influence of step edge barriers and grain boundaries of molecular thin films on the various scaling exponent values were elucidated. The simulation results for the scaling exponents were also well consistent with the experimental data for previously reported molecular thin film systems.

• Journal of The Korean Astronomical Society
• /
• v.37 no.4
• /
• pp.223-224
• /
• 2004

The Tycho supernova remnant (SNR), as one of the few historical SNRs, has been widely studied in various wavebands and previous observations have shown evidence that Tycho is interacting with a dense ambient medium toward the northeast direction, In this paper, we report our high-resolution (16') $^{12}CO$ observation of the remnant using the Nobeyama 45m radio telescope. The Nobeyama data shows that a large molecular cloud surrounds the SNR along the northeastern boundary. We suggest that the Tycho SNR and the molecular cloud are both located in the Perseus arm and that the dense medium interacting with the SNR is possibly the molecular cloud. We also discuss the possible connection between the molecular cloud and the Balmer-dominated optical filaments, and suggest that the preshock gas may be accelerated within the cosmic ray and/or fast neutral precursor.