Discovering myself and being an ambassador

My Proposed Culminating Experience was creating an album that can introduce the culture of South Korea to the world. I want to be a music ambassador to the people around the world because I believe that South Korea has great philosophy towards all mankind from five thousand years ago. My goal for this project was to create pieces to express my thought towards this competitive society and give a better suggestion for human being to live coexistence.https://remix.berklee.edu/graduate-studies-global-jazz/1018/thumbnail.jp

TRANSCRIPTION FACTOR-DNA INTERACTIONS: INVESTIGATING BINDING SPECIFICITIES IN BASE-RESOLUTION MODELS

50 pagesThe epigenome is a multitude of all molecular interactions that governs genome regulatory activities. Sequence-specific transcription factors (TFs) are the key regulators that control gene expression by binding to specific DNA sequences at promoters or distal enhancers. Understanding how TFs recognize their DNA binding sites forms the basis for understanding mechanisms of transcriptional control. Technological developments have led to the identification of TF binding preferences and revealed how TF-DNA interactions, local DNA structure, and genomic features influence TF-DNA binding. Yet, a precise human epigenome remains largely undefined. Mechanistic insights into how transcription factors recognize their cognate sites across a genome may be best understood through a combination of in vivo and in vitro genome-wide binding measurements. To this end, I provided the first single base pair measurements of human stem cell factor KLF4 binding to a noncognate DNA sites in vivo. To further explore the mechanistic basis for such interactions, I initiated development of an in vitro biochemically defined system for measuring protein-DNA interactions genome-wide for human TFs. In the first stage of this process, I developed methods to express human TFs using in vitro transcription/ translation systems as well as an E. coli T7 expression system. By using His-GFP fusions to these TFs, I tracked their production and purification in real time using GFP’s intrinsic fluorescence. I then explored whether His-GFP can be used to establish an in vitro genome-wide assay for site-specific DNA binding (PB-exo assay), where nickel resin is used to retain His-tagged proteins, and GFP is used track binding in real time. Collectively, I demonstrated the feasibility of in vitro protein expression and purification as applied towards the PB-exo assay, including using nickel resin in place of antibodies to immunoprecipitated target proteins. The work here provides several concrete steps towards developing a genome-wide assay for in vitro protein-DNA interactions of human TFs

Development of a Real-Time Virtual Nitric Oxide Sensor for Light-Duty Diesel Engines

This study describes the development of a semi-physical, real-time nitric oxide (NO) prediction model that is capable of cycle-by-cycle prediction in a light-duty diesel engine. The model utilizes the measured in-cylinder pressure and information obtained from the engine control unit (ECU). From the inputs, the model takes into account the pilot injection burning and mixing, which affects the in-cylinder mixture formation. The representative in-cylinder temperature for NO formation was determined from the mixture composition calculation. The selected temperature and mixture composition was substituted using a simplified form of the NO formation rate equation for the cycle-by-cycle estimation. The reactive area and the duration of NO formation were assumed to be limited by the fuel quantity. The model predictability was verified not only using various steady-state conditions, including the variation of the EGR rate, the boost pressure, the rail pressure, and the injection timing, but also using transient conditions, which represent the worldwide harmonized light vehicles test procedure (WLTC). The WLTC NO prediction results produced less than 3% error with the measured value. In addition, the proposed model maintained its reliability in terms of hardware aging, the changing and artificial perturbations during steady-state and transient engine operations. The model has been shown to require low computational effort because of the cycle-by-cycle, engine-out NO emission prediction and control were performed simultaneously in an embedded system for the automotive application. We expect that the developed NO prediction model can be helpful in emission calibration during the engine design stage or in the real-time controlling of the exhaust NO emission for improving fuel consumption while satisfying NO emission legislation

Interinstitutional Research Team Formation Based on Bibliographic Network Embedding

This study aims at forming research teams for interinstitutional collaborations. Research institutes have their own purposes and topics of interest. Thus, supporting joint research between multiple institutes, we have to consider not only synergies between scholars but also purposes of the institutes. To solve this problem, we propose a bibliographic network embedding method that can learn characteristics of institutes, not only of each scholar. First, we compose a bibliographic network that consists of scholars, publications, venues, research projects, and institutes. Collaboration styles and research topics of institutes and scholars are extracted by mining subgraphs from the bibliographic network. Then, vector representations of network nodes are learned based on occurrences of subgraphs on the nodes and neighborhoods of the nodes. Based on the vector representations, we train multilayer perceptrons (MLP) to assess collaboration probability between scholars affiliated in different institutes. For training the MLP, we suggest three strategies: (i) considering every collaboration, (ii) focusing on interinstitutional collaborations, and (iii) focusing on collaboration outcomes. To evaluate the proposed methods, we have analyzed research collaborations of POSTECH (Pohang University of Science and Technology) and RIST (Research Institute of Industrial Science and Technology) from 2011 to 2020. Then, we conducted the research team formation for joint research of the two institutes according to two purposes: pure research and commercialization research

eRNA co-expression network uncovers TF dependency and convergent cooperativity

Abstract Enhancer RNAs (eRNAs) are non-coding RNAs produced by transcriptional enhancers that are highly correlated with their activity. Using a capped nascent RNA sequencing (PRO-cap) dataset in human lymphoblastoid cell lines across 67 individuals, we identified inter-individual variation in the expression of over 80 thousand transcribed transcriptional regulatory elements (tTREs), in both enhancers and promoters. Co-expression analysis of eRNAs from tTREs across individuals revealed how enhancers are associated with each other and with promoters. Mid- to long-range co-expression showed a distance-dependent decay that was modified by TF occupancy. In particular, we found a class of “bivalent” TFs, including Cohesin, that both facilitate and isolate the interaction between enhancers and/or promoters, depending on their topology. At short distances, we observed strand-specific correlations between nearby eRNAs in both convergent and divergent orientations. Our results support a cooperative model of convergent eRNAs, consistent with eRNAs facilitating adjacent enhancers rather than interfering with each other. Therefore, our approach to infer functional interactions from co-expression analyses provided novel insights into the principles of enhancer interactions as a function of distance, orientation, and binding landscapes of TFs

Perception of bullying-like phenomena in South Korea: a qualitative approach from a lifespan perspective

This study investigates perceptions of bullying-like behaviours in South Korea,from young children to adults, using a qualitative approach. Focus groups were conducted across different age ranges, from preschool to workplace employees. 113 participants were shown cartoons or descriptions of negative behaviours and asked ‘why these happened’, and ‘what do you think about them’. Interview transcripts were analysed by grounded theory. Similarities and differences across ages were found for two themes, origin and judgment of behaviours. Situational and interpersonal factors were seen as important in causing the behaviours, both in school and workplace. 15-17 year old pupils and mothers considered the behaviours less acceptable than younger pupils; whereas 10-15 year old pupils and workplace employees showed more justification of the behaviours and were more likely to attribute the situation to victim’s responsibility. The findings are discussed in relation to similar phenomena in western cultures, and the particular nature of Korean bullying or wang-ta

Development of semi-empirical soot emission model for a CI engine

Soot is one of the main harmful emissions of diesel engines that is mainly generated in the reacting fuel jet of diesel injection. Over 99% of the engine-out soot can be filtered by a diesel particulate filter (DPF). However, when the soot load of the DPF is high, a regeneration process that oxidizes the accumulated soot reduces fuel economy. A real-time soot estimation model can contribute to real-time feedback soot control under transient conditions to minimize the engine-out soot emission and frequency of DPF regeneration. A zero-dimensional engine-out soot estimation model for a diesel engine is developed in this study. The semi-empirical soot model considers both the formation and oxidation of soot. In the model, soot formation was correlated with the cross-sectional average equivalence ratio at the lift-off length of the fuel spray. The equivalence ratio at the lift-off length is an indicator of how much air and vaporized fuel are mixed as the fuel reaches the reaction zone. The mass of the injected fuel and combustion duration were also correlated with soot formation. The Nagle and Strickland Constable mechanism, which calculates the soot oxidation rate was correlated with the soot oxidation in this study. The results of the soot estimation showed an R-2 of 0.901 and root mean square error of 10.8 mg/m(3) for steady-state experimental cases. The engine-out soot model was also combined with the in-cylinder pressure model proposed by the authors, and validated through the transient Worldwide Harmonized Light Vehicles Test Cycle (WLTC) mode. The estimates agreed with the measured soot, with an accumulated soot error of approximately 6% during the WLTC, even without using an in-cylinder pressure sensor. The soot model developed in this study can help minimize tailpipe-out soot emissions and improve fuel economy by influencing the real-time feedback control during transient and frequent DPF regeneration.N

Numerical Analysis of the Combustion and Emission Characteristics of Diesel Engines with Multiple Injection Strategies Using a Modified 2-D Flamelet Model

The multiple injection strategy has been widely used in diesel engines to reduce engine noise, NOx and soot formation. Fuel injection developments such as the common-rail and piezo-actuator system provide more precise control of the injection quantity and time under higher injection pressures. As various injection strategies become accessible, it is important to understand the interaction of each fuel stream and following combustion process under the multiple injection strategy. To investigate these complex processes quantitatively, numerical analysis using CFD is a good alternative to overcome the limitation of experiments. A modified 2-D flamelet model is further developed from previous work to model multi-fuel streams with higher accuracy. The model was validated under various engine operating conditions and captures the combustion and emissions characteristics as well as several parametric variations. The model is expected to be used to suggest advanced injection strategies in engine development processes