Publications

2025

[A] H. Kim,* S. T. Mergelsberg, M. S. Chun, G. W. Buchko, & B. Ginovska,* Submitted

• Hoshin Kim is a first and co-corresponding author

2024

[27] S. T. Mergelsberg, H. Kim, G. W. Buchko, & B. Ginovska, "SAXS of murine amelogenin identifies a persistent dimeric species from pH 5.0 to 8.0" Journal of Structural Biology, 216, 4, (2024): 108131 [Link]

[26] N. Srividya, H. Kim, S. Raugei, & B. M. Lange, "Chemical diversity in angiosperms - monoterpene synthases control complex reactions that provide the precursors for ecologically and commercially important monoterpenoids" The Plant Journal, 119, 1, (2024): 28-55 [Link]

[25] H. Kim, B. L. Gorman, M. J. Taylor, & C. R. Anderton, "Atomistic simulations for investigation of substrate and salt effect on lipid in-source fragmentation in secondary ion mass spectrometry: A follow-up study" Biointerphases, 19, 1, (2024): 011003 [Link]

• Journal Cover

[24] J. A. Richardson, H. Kim, J. J. Kas, X. You, A. Andersen, B. Ginovska, A. Bhattacharjee, & R. Sarangi, "X-ray absorption spectroscopy and theoretical investigations of the effect of extended ligands in potassium organic matter interaction" Journal of Chemical Physics, 160, (2024): 044114 [Link]

2023

[23] D. M. Rodriguez,# H. Kim,# N. Sadler, X. Li, P. Bohutskyi, M. Valiev, W.-J. Qian, & M. S. Cheung, "PTM-Psi: A Python package to facilitate the computational investigation of post-translational modification on protein structures and their impacts on dynamics and functions" Protein Science, 32, 12, (2023): e4822 [Link]

• #Daniel Mejia Rodriguez and Hoshin Kim - Equally Contributed

• Software PTM-Psi has been released and is available on [GitHub]

• PTM-Psi has been reported on DOE CODE [Link] (DOI: https://doi.org/10.11578/dc.20230703.1)

• This published study has been featured on the "Science Highlights" Page on the PNNL website [Link]

[22] M. J. Taylor, H. Kim, W. Kew, A. Andersen, A. Bhattacharjee, M. H. Engelhard, & C. R. Anderton, "Atomistic simulations for investigation of substrate effects on lipid in-source fragmentation in secondary ion mass spectrometry"  Biointerphases, 18, 1, (2023): 011003 [Link]

• This published study has been selected as the "Featured Article" 

• Journal Cover

• This paper is a part of the Biointerphases Special Topic Collection on Tutorials in Secondary Ion Mass Spectrometry (SIMS)

2022

[21] H. Kim, D. G. Hauner, J. A. Laureanti, K. Agustin, S. Raugei, & N. Kumar, "Mechanistic Investigation of SARS-CoV-2 Main Protease to Accelerate Design of Covalent Inhibitors" Scientific Reports, 12, (2022): 21037 [Link]

[20] H. Kim, N. Srividya, I. Lange, E. W. Huchala, B. Ginovska, B. M. Lange, and S. Raugei, "Determinants of Selectivity for the Formation of Monocyclic and Bicyclic Products in Monoterpene Synthases" ACS Catalysis, 12, 12, (2022): 7453-7469 [Link]

• This published study has been featured on the "Research Highlights" Page on the PNNL website [Link]

• Also, featured on [LinkedIn] [Facebook]

2021

[19] T. J. Oweida, H. S. Kim, J. Donald, A. Singh, & Y. G. Yingling "Assessment of AMBER force fields for capturing ssDNA structure" Journal of Chemical Theory and Computation,  17, 2, (2021): 1208–1217 [Link]

2020

[18] M.J. Umerani, P Pratakshya, A. Chatterjee, J. A. Cerna, H. S. Kim, G. Ilc, M.kovacic, C. Magnan, B. Marmiroli, B. Satori, A. L. Kwansa, H. Orins, A. W. Bartlett, E. M. Leung, Z. Feng, K. L. Naughton, B. Norton-Baker, L. Phan, J. Long, A. Allevato, J. E. Leal-Cruz, Q. Lin, P. Baldi, S. Bernstorff, J Plavec, Y. G. Yingling, & A. A. Gorodetsky "Structure, self-assembly, and properties of a truncated reflectin variant" Proceedings of the National Academy of Sciences of the United States of America, 117, 52 (2020): 32891-32901 [Link]

[17] A. Singh, A. L. Kwansa, H. S. Kim, J. T. Williams, H. Yang, N. K. Li, J. D. Kubicki, A. W. Roberts, C. H. Haigler, & Y. G. Yingling "In silico prediction of full-length integral membrane protein structure, cotton cellulose synthase (GhCESA1), and its hierarchical complexes" Cellulose, 27 (2020): 5597–5616    [Link]

[16] H. S. Kim,# N. A. Brown,#, Stefan Zauscher, & Y. G. Yingling. "Effect of octadecylamine surfactant concentration on DNA interactions with graphene surfaces" Langmuir, 36, 4 (2020): 931-938    [Link]

• #Ho Shin Kim and Nate A Brown - Equally Contributed

2018

[15] R. Xiong, H. S. Kim, L. Zhang, V. F. Korolovych, S. Zhang, Y. G. Yingling, & V. V. Tsukruk. "Wrapping nanocellulose nets around graphene oxide sheets" Angewandte Chemie International Edition, 57 (2018): 1-7   [Link]

[14] H. S. Kim,# T. J. Oweida,# & Y. G. Yingling. "Interfacial stability of graphene-based surfaces in water and organic solvents" Journal of Materials Science, 53, 8 (2018): 5766-5776   [Link]

•  #Ho Shin Kim and Thomas J. Oweida - Equally contributed

• This paper is selected as the finalist for 2018 Cahn Prize & the best paper in April, 2018 issue. [Link]

2017

[13] R. Xiong, H. S. Kim, S. Zhang, S. Kim, V. F. Korolovych, R. Ma, Y. G. Yingling, C. Lu, & V. V. Tsukruk. "Template-guided assembly of silk fibroin on cellulose nanofibers for robust nanostructures with ultrafast water transport", ACS Nano, 11, 12 (2017): 12008-12019   [Link]

[12] H. S. Kim, B. L. Farmer, & Y. G. Yingling. “Effect of graphene oxidation rate on adsorption of poly-thymine single stranded DNA”, Advanced Materials Interfaces, 4, 8 (2017): 1601168   [Link]

•  Journal Cover 

[11] Q. Tu,# H. S. Kim,# T. J. Oweida, Z. Parlak, Y. G. Yingling, & S. Zauscher. “Interfacial mechanical properties of graphene on self-assembled monolayers: experiments and simulations”, ACS Applied Materials & Interfaces, 9, 11 (2017): 10203-10213   [Link]

• #Qing Tu and Ho Shin Kim - Equally contributed

[10] J. A. Nash, A. L. Kwansa, J. S. Peerless, H. S. Kim, & Y. G. Yingling. “Advances in molecular modeling of nanoparticle-nucleic acid interfaces", Bioconjugate Chemistry, 28, 1 (2017): 3-10   [Link]

• Journal Cover

2016

[09] B. Roark, J. A. Tan, A. Ivanina, M. Chandler, J. Castaneda, H. S. Kim, S. Jawahar, M. Viard, S. Talic, K. L. Wustholz, Y. G. Yingling, M. Jones, & K. A. Afonin. "Fluorescence blinking as an output signal for programmable biosensing", ACS Sensors, 1, 11 (2016): 1295-1300   [Link]

[08] A. M. Grant, H. S. Kim, T. L. Dupnock, K. Hu, Y. G. Yingling, & V. V. Tsukruk. “Silk fibroin–substrate interactions at heterogeneous nanocomposite interfaces”, Advanced Functional Materials 26, 35 (2016): 6380-6392   [Link]

•  Journal Cover

[07] H. S. Kim, D. Eom, Y. M. Koo, & Y. G. Yingling. “Role of imidazolium cation on structure and activity of Candida antarctica lipase B enzyme in ionic liquids”, Physical Chemistry Chemical Physics 18, 32 (2016): 22062-22069   [Link] 

•  Journal Cover

[06] H. S. Kim, S. M. Huang, & Y. G. Yingling. “Sequence dependent interaction of single stranded DNA with graphitic flakes: atomistic molecular dynamics simulations”, MRS Advances 1, 25 (2016): 1883-1889   [Link] 

2015

[05] S. K. Clendennen, Y. G. Yingling, & H. S. Kim, “CALB variants”, US Patent, 14/961,237 (2015)    [Link] 

• Application granted in 2018

2014

[04] N. K. Li, H. S. Kim, J. A. Nash, M. Lim, & Y. G. Yingling. "Progress in molecular modelling of DNA materials." modelling of DNA materials." Molecular Simulation, 40, (2014): 1-7   [Link]

[03] H. S. Kim, S. H. Ha, L. Sethaphong, Y. M. Koo, & Y. G. Yingling. "The relationship between enhanced enzyme activity and structural dynamics in ionic liquids: a combined computational and experimental study." Physical Chemistry Chemical Physics 16, 7 (2014): 2944-2953   [Link]

2012

[02] H. S. Kim & Y. M. Koo. "Effects of physicochemical properties of ionic liquids on butyl acetate synthesis using Candida antarctica lipase B." Korean Journal of Chemical Engineering 29, 11 (2012): 1610-1614    [Link]

[01] H. S. Kim, R. Pani, S. H. Ha, Y. M. Koo, & Y. G. Yingling. "The role of hydrogen bonding in water-mediated glucose solubility in ionic liquids." Journal of Molecular Liquids 166 (2012): 25-30   [Link]