Browsing by Author "Park, J."

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    BLEND: A fast, memory-efficient and accurate mechanism to find fuzzy seed matches in genome analysis
    (Oxford University Press, 2023-01-10) Firtina, C.; Park, J.; Alser, M.; Kim, J. S.; Cali, D. S.; Shahroodi, T.; Ghiasi, N. M.; Singh, G.; Kanellopoulos, K.; Alkan, Can; Mutlu, O.
    Generating the hash values of short subsequences, called seeds, enables quickly identifying similarities between genomic sequences by matching seeds with a single lookup of their hash values. However, these hash values can be used only for finding exact-matching seeds as the conventional hashing methods assign distinct hash values for different seeds, including highly similar seeds. Finding only exact-matching seeds causes either (i) increasing the use of the costly sequence alignment or (ii) limited sensitivity. We introduce BLEND, the first efficient and accurate mechanism that can identify both exact-matching and highly similar seeds with a single lookup of their hash values, called fuzzy seed matches. BLEND (i) utilizes a technique called SimHash, that can generate the same hash value for similar sets, and (ii) provides the proper mechanisms for using seeds as sets with the SimHash technique to find fuzzy seed matches efficiently. We show the benefits of BLEND when used in read overlapping and read mapping. For read overlapping, BLEND is faster by 2.4×-83.9× (on average 19.3×), has a lower memory footprint by 0.9×-14.1× (on average 3.8×), and finds higher quality overlaps leading to accurate de novo assemblies than the state-of-the-art tool, minimap2. For read mapping, BLEND is faster by 0.8×-4.1× (on average 1.7×) than minimap2. Source code is available at https://github.com/CMU-SAFARI/BLEND. © 2023 The Author(s). Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.
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    Instability of a noncrystalline NaO2 film in Na-O2 batteries: The controversial effect of the RuO2 catalyst
    (American Chemical Society, 2018) Tovini, M. F.; Hong, M.; Park, J.; Demirtaş, M.; Toffoli, D.; Ustunel, H.; Byon, H. R.; Yılmaz, E.
    The unique electrochemical and chemical features of sodium-oxygen (Na-O2) batteries distinguish them from the lithium-oxygen (Li-O2) batteries. NaO2 as the main discharge product is unstable in the cell environment and chemically degrades, which triggers side products' formation and charging potential increment. In this study, RuO2 nanoparticles dispersed on carbon nanotubes (CNTs) are used as the catalyst for Na-O2 batteries to elucidate the effect of the catalyst on these complex electrochemical systems. The RuO2/CNT contributes to the formation of a poorly crystalline and coating-like NaO2 structure during oxygen reduction reaction, which is drastically different from the conventional micron-sized cubic NaO2 crystals deposited on the CNT. Our findings demonstrate a competition between NaO2 and side products' decompositions for RuO2/CNT during oxygen evolution reaction (OER). We believe that this is due to the lower stability of a coating-like NaO2 because of its noncrystalline nature and high electrode/electrolyte contact area. Although RuO2/CNT catalyzes the decomposition of side products at a lower potential (3.66 V) compared to CNT (4.03 V), it cannot actively contribute to the main electrochemical reaction of the cell during OER (NaO2 → Na+ + O2 + e-) because of the fast chemical degradation of the film NaO2 to the side products. Therefore, tuning the morphology and crystallinity of NaO2 by a catalyst is detrimental for the Na-O2 cell performance and it should be taken into account for the future applications.
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    Lateral overgrowth of germanium for monolithic integration of germanium-on-insulator on silicon
    (Elsevier, 2015) Hyung Nam J.; Alkis, S.; Nam, D.; Afshinmanesh F.; Shim J.; Park, J.; Brongersma, M.; Okyay, Ali Kemal; Kamins, T.I.; Saraswat, K.
    A technique to locally grow germanium-on-insulator (GOI) structure on silicon (Si) platform is studied. On (001) Si wafer, silicon dioxide (SiO2) is thermally grown and patterned to define growth window for germanium (Ge). Crystalline Ge is grown via selective hetero-epitaxy, using SiO2 as growth mask. Lateral overgrowth of Ge crystal covers SiO2 surface and neighboring Ge crystals coalesce with each other. Therefore, single crystalline Ge sitting on insulator for GOI applications is achieved. Chemical mechanical polishing (CMP) is performed to planarize the GOI surface. Transmission electron microscopy (TEM) analysis, Raman spectroscopy, and time-resolved photoluminescence (TRPL) show high quality crystalline Ge sitting on SiO2. Optical response from metal-semiconductor-metal (MSM) photodetector shows good optical absorption at 850 nm and 1550 nm wavelength. © 2015 Elsevier B.V. All rights reserved.