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Search Results: 1 - 10 of 37886 matches for " Han Seul Kim "
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Recent progress in atomistic simulation of electrical current DNA sequencing
Han Seul Kim,Yong-Hoon Kim
Physics , 2014, DOI: 10.1016/j.bios.2015.02.020
Abstract: We review recent advances in the DNA sequencing based on the measurement of transverse electrical currents. Device configurations proposed in the literature are classified according to whether the molecular fingerprints appear as the major (Mode I) or perturbing (Mode II) current signals. Scanning tunneling microscope and tunneling electrode gap configurations belong to the former category, while the nanochannels with or without an embedded nanopore belong to the latter. The molecular sensing mechanisms of Modes I and II roughly correspond to the electron tunneling and electrochemical gating, respectively. Special emphasis will be given on the computer simulation studies, which have been playing a critical role in the initiation and development of the field. We also highlight low-dimensional nanomaterials such as carbon nanotubes, graphene, and graphene nanoribbons that allow the novel Mode II approach. Finally, several issues in previous computational studies are discussed, which points to future research directions toward more reliable simulation of electrical current DNA sequencing devices.
Prediction of ultra-high ON/OFF ratio nanoelectromechanical switching from covalently-bound C60 chains
Han Seul Kim,Jhinhwan Lee,Yong-Hoon Kim
Physics , 2013, DOI: 10.1016/j.carbon.2013.09.054
Abstract: Applying a first-principles computational approach, we have systematically analyzed the effects of [2+2] cycloaddition oligomerization of fullerene C60 chains on their junction electronic and charge transport properties. For hypothetical infinite C60 chains, we first establish that the polymerization can in principle increase conductance by several orders of magnitude due to the strong orbital hybridizations and band formation. On the other hand, our simulations of the constant-height scanning tunneling microscope (STM) configuration shows that, in agreement with the recent experimental conclusion, the junction electronic structure and device characteristics are virtually unaffected by the C60 chain oligomerization. We further predict that the switching characteristics including even the ON/OFF-state assignment will sensitively depend on the substrate metal species due to the Fermi-level pinning at the substrate-side contact and the subsequent energy level bending toward the STM tip-side contact. We finally demonstrate that a force-feedbacked nanoelectromechanical approach in which both of the C60-electrode distances are kept at short distances before and after switching operations can achieve a metal-independent and significantly improved switching performance due to the Fermi-level pinning in both contacts and the large intrinsic conductance switching capacity of the C60 chain oligomerization.
Distinct mechanisms of DNA sensing based on N-doped carbon nanotubes with enhanced conductance and chemical selectivity
Han Seul Kim,Seung Jin Lee,Yong-Hoon Kim
Physics , 2012, DOI: 10.1002/smll.201301225
Abstract: Carrying out first-principles calculations, we study N-doped capped carbon nanotube (CNT) electrodes applied to DNA sequencing. While we obtain for the face-on nucleobase junction configurations a conventional conductance ordering where the largest signal results from guanine according to its high highest occupied molecular orbital (HOMO) level, we extract for the edge-on counterparts a distinct conductance ordering where the low-HOMO thymine provides the largest signal. The edge-on mode is shown to operate based on a novel molecular sensing mechanism that reflects the chemical connectivity between N-doped CNT caps that can act both as electron donors and electron acceptors and DNA functional groups that include the hyperconjugated thymine methyl group.
Atomistic Mechanisms of Codoping-Induced p- to n-Type Conversion in Nitrogen-Doped Graphene
Hyo Seok Kim,Han Seul Kim,Seong Sik Kim,Yong-Hoon Kim
Physics , 2014, DOI: 10.1039/c4nr05024j
Abstract: It was recently shown that nitrogen-doped graphene (NG) can exhibit both p- and n-type characters depending on the C-N bonding nature, which represents a significant bottleneck for the development of graphene-based electronics. Based on first-principles calculations, we herein scrutinise the correlations between atomic and electronic structures of NG, and particularly explore the feasibility of converting p-type NG with pyridinic, pyrrolic, and nitrilic N into n- or bipolar type by introducing an additional dopant atom. Out of the nine candidates, B, C, O, F, Al, Si, P, S, and Cl, we find that the B-, Al-, and P-codoping can anneal even relatively large vacancy defects in p-type NG. It will be also shown that, while the NG with pyridinic N can be converted into n-type via codoping, only the bipolar type conversion can be achieved for the NG with nitrilic or pyrrolic N. The amount of work function reduction was up to 0.64 eV for the pyridinic N next to a monovacancy. The atomistic origin of such diverse type changes is analysed based on Mulliken and crystal orbital Hamiltonian populations, which provide us with a framework to connect the local bonding chemistry with macroscopic electronic structure in doped and/or defective graphene. Moreover, we demonstrate that the proposed codoping scheme can recover the excellent charge transport properties of pristine graphene. Both the type conversion and conductance recovery in codoped NG should have significant implications for the electronic and energy device applications.
Conductance recovery and spin polarization in boron and nitrogen codoped graphene nanoribbons
Seong Sik Kim,Han Seul Kim,Hyo Seok Kim,Yong-Hoon Kim
Physics , 2014,
Abstract: We present an ab initio study of the structural, electronic, and quantum transport properties of B-N-complex edge-doped graphene nanoribbons (GNRs). We find that the B-N edge codop-ing is energetically a very favorable process and furthermore can achieve novel doping effects that are absent for the single B or N doping. The compensation effect between B and N is predicted to generally recover the excellent electronic transport properties of pristine GNRs. For the zigzag GNRs, however, the spatially localized B-N defect states selectively destroy the doped-side spin-polarized GNR edge currents at the valence and conduction band edges. We show that the energetically and spatially spin-polarized currents survive even in the fully ferromagnetic metallic state and heterojunction configurations. This suggests a simple yet ef-ficient scheme to achieve effectively smooth GNR edges and graphene-based spintronic de-vices.
Carbon nanobuds based on carbon nanotube caps: A first-principles study
Ji Il Choi,Hyo Seok Kim,Han Seul Kim,Ga In Lee,Jeung Ku Kang,Yong-Hoon Kim
Physics , 2015, DOI: 10.1039/C5NR07188G
Abstract: Based on density functional theory calculations, we here show that the formation of a fullerene C$_{60}$ carbon "nanobud" (CNB) on carbon nanotube (CNT) caps is energetically more favorable than that on CNT sidewalls. The dominant CNB formation mode for CNT caps is found to be the [2+2] cycloaddition reaction as in the conventional CNT sidewall case. However, it is identified to be exothermic in contrast to the endothermic reaction on CNT sidewalls. Computed reaction pathways further demonstrate that the formation (dissociation) barrier for the CNT cap-based CNB is slightly lower (significantly higher) than that of the CNT sidewall-based CNB, indicating an easier CNB formation as well as a higher structural stability. Additionally, performing matrix Green's function calculations, we study the charge transport properties of the CNB/metal electrode interfaces, and show that the C$_{60}$ bonding to the CNT cap or open end induces resonant transmissions near the Fermi level. It is also found that the good electronic linkage in the CNT cap-C$_{60}$ cycloaddition bonds results in the absence of quantum interference patterns, which contrasts the case of the CNB formed on an open-ended CNT that shows a Fano resonance profile.
Low-density lipoprotein particle size in hepatic steatosis and metabolic syndrome
Dal-Sik Kim, Young-Kon Kim, Do-Sung Kim, Han-Jung Chae, Tae-Sun Park, Young I Cho, Seul-Ki Jeong
Diabetology & Metabolic Syndrome , 2010, DOI: 10.1186/1758-5996-2-18
Abstract: Carotid intima-media thickness (IMT) and plaque formation, and HS were diagnosed ultrasonographically, and the MetS was diagnosed using the ATP III criteria in 274 healthy workers (mean age ± SD, 43.5 ± 7.1 yrs). LDL particle size was measured with density gradient ultracentrifugation, and subfractions were classified as large, buoyant LDL I (27.2~28.5 nm) and small, dense LDL III (24.2~25.5). All participants were grouped into three categories: control, subjects with HS alone and those with both HS and the MetS.The subjects with HS alone were 84 (30.7%), whereas those with HS and the MetS were 46 (16.8%). LDL peak particle sizes showed significant negative correlations with carotid mean IMTs. LDL peak particle size and LDL I (%) decreased significantly in the HS, showing the lowest values in the subjects with both HS and the MetS, and their association was independent, even adjusted for potential confounders. LDL III also showed independent associations across the groups.HS alone was more prevalent than HS combined with the MetS in general population. For the patients with HS alone, LDL particle size and carotid atherosclerosis were found to fall in the middle of the control and those with both HS and the MetS.Atherosclerosis and its relevant vascular events including cardiovascular disease (CVD), stroke, and peripheral arterial disease (PAD) have become a leading cause of disability and mortality in modern society [1]. Increasing trends of the vascular diseases are universal both in developed and developing countries [2]. A lifestyle summarized as a lack of physical activity and moderate-to-high intake of calories seems to be one of the most important causes of rapidly increasing prevalence of the metabolic syndrome (MetS) [3], type 2 diabetes mellitus (DM) [4], dyslipidemia [5], and eventually atherothrombotic diseases [2].The sedentary lifestyle made people more dyslipidemic; atherogenic dyslipidemia, consisting of high triglyceride (TG), low high-density lipopr
Effect of Maltose Concentration on Plant Regeneration of Anther Culture with Different Genotypes in Rice (Oryza sativa L.)  [PDF]
Seul Gi Park, Mohammad Ubaidillah, Kyung-Min Kim
American Journal of Plant Sciences (AJPS) , 2013, DOI: 10.4236/ajps.2013.411279
Abstract:

This study describes the impact of different concentrations of maltose on plant regeneration of anther culture for five genotypes of rice (Oryza sativa). N6 medium was used for calli induction, while N6 medium supplemented with different concentrations of maltose, 2.0 mg/L NAA and 0.5 mg/L kinase was used for plant regeneration. The result showed that during the initial stages of calli induction the anther cultures had varying rates of calli formation among genotypes, with the best frequency being observed for Dreami2/CaMsrB2-8-DH-1 with a calli frequency of 27.8%. Different genotypes of rice cultured in regeneration media showed varying plantlet regeneration on media supplemented with different concentrations of maltose, with low concentrations (0.04 g/L) leading to low frequency regeneration plantlet but high green plant production. Indeed, when Dreami2/CaMsrB2-8-DH-2 and Dreami2/CaMsrB2-8-DH-5 were cultivated under these conditions, 100% green plants were observed. Another genotype also showed a small rate of albino frequency in response to the lowest concentration of maltose, while increased maltose concentrations

Vegetation of mono-layer landfill cover made of coal bottom ash and soil by compost application  [PDF]
Seul Bi Lee, Sang Yoon Kim, Chan Yu, Soon-Oh Kim, Pil Joo Kim
Journal of Agricultural Chemistry and Environment (JACEN) , 2013, DOI: 10.4236/jacen.2013.23008
Abstract: Monolayer barriers called evapotranspiration (ET) covers were developed as alternative final cover systems in waste landfills but high-quality soil remains a limiting factor in these cover systems. Coal bottom ash was evaluated to be a very good alternative to soil in previous tests and a combination of soil (65% wt.wt-1) and coal bottom ash (35% wt.wt-1) was evaluated to be the most feasible materials for ET cover systems. In our pot test, selected manure compost as soil amendment for the composite ET cover system, which was made of soil and bottom ash at ca. 40 Mg.ha-1 application level was very effective to promote vegetation growth of three plants; namely, garden cosmos (Cosmosbipinnatus), Chinese bushclover (Lespedezacuneata), and leafy lespedeza (Lespedeza cyrtobotrya). To evaluate the effect of compost application on plant growth in an ET vegetative cover system, two couples of lysimeters, packed with soil and a mixture of soil and bottom ash, were installed in a pilot landfill cover system in 2007. Manure composts were applied at the rates of 0 and  40 Mg.ha-11before sowing the five plant species, i.e.indigo-bush (Amorphafruticosa), Japanese mugwort (Artemisia princeps, Arundinella hirta, Lespedezacuneata, and Lespedezacyrtobotrya). Unseeded native plant (green foxtail,Setaria viridis) was dominant in all treatments in the 1st year after installation while the growth of the sown plants significantly improved over the years. Total biomass productivity significantly increased with manure compost application, and more significantly increased in the composite ET cover made of soil and bottom ash treatment compared to the single soil ET cover, mainly due to more improved soil nutrient levels promoting vegetation growth and maintaining the vegetation system. The use of bottom ash as a mixing material in ET cover systems has a strong potential as an alternative to fine-grained soils, and manure compost addition can effectively enhance vegetative propagation in ET cover systems.
Effect of Korean Herbal Medicine Combined with a Probiotic Mixture on Diarrhea-Dominant Irritable Bowel Syndrome: A Double-Blind, Randomized, Placebo-Controlled Trial
Seok-Jae Ko,Gajin Han,Seul-Ki Kim,Jae-Gu Seo,Won-Seok Chung,Bongha Ryu,Jinsung Kim,Inkwon Yeo,Beom-Joon Lee,Jin-Moo Lee,Jae-Woo Park
Evidence-Based Complementary and Alternative Medicine , 2013, DOI: 10.1155/2013/824605
Abstract: Introduction. Although combination therapy with herbal medicine and probiotics is gaining popularity for controlling diarrhea-dominant irritable bowel syndrome (D-IBS) symptoms, few studies have investigated its clinical effects. Materials and Methods. Fifty-three patients with D-IBS were randomly allocated into 1 of the following 4 groups: herbal medicine (Gwakhyangjeonggisan; GJS) plus probiotics (Duolac7S; DUO), GJS plus placebo DUO, placebo GJS plus DUO, and placebo GJS plus placebo DUO. The study period consisted of a 2-week run-in, 8 weeks of administration, and 2 weeks of follow-up. The primary outcomes were weekly adequate relief (AR) of overall IBS symptoms and the proportion of responders (PR) during the administration period. The secondary outcomes included individual IBS symptoms, stool assessment, and quality of life. Changes of intestinal microbiota and intestinal permeability were also analyzed. Results and Discussion. Weekly AR was not different among the 4 groups throughout the treatment period. However, the 3 treatment groups exhibited significant improvements in PR compared to the findings in the placebo group. In the intestinal microbiota assessment, herbal medicine and probiotics synergistically increased beneficial bacteria counts. Conclusion. Combination therapy with herbal medicine and probiotics appears to relieve overall IBS symptoms by synergistically increasing beneficial intestinal microbe counts. 1. Introduction Irritable bowel syndrome (IBS) is a functional gastrointestinal disorder characterized by abdominal pain, discomfort, and bowel disturbances without any structural abnormality [1]. IBS may cause significant inconvenience to patients, impair their social functioning, and deteriorate their quality of life [2]. The involvement of various factors in the pathophysiology of IBS makes treatment more difficult [3]. Factors such as imbalances of intestinal microbiota and increased intestinal permeability have been identified as important elements in the pathophysiology of IBS [4, 5]. Therefore, therapeutic approaches aimed at resolving disturbances in the intestinal microbiota and maintaining mucosal barrier homeostasis can be helpful in the treatment of IBS. However, due to dissatisfying results with conventional IBS treatments, complementary therapies including herbal medicine and probiotics are becoming attractive options for many patients [6]. Herbal medicines have long been used in Asian countries due to their safety and having only a few side effects. Gwakhyangjeonggisan (GJS; Kkako-shoki-san in Kampo Medicine;
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