Publications — BTG @ PKNU

2026 01 article

01

Advances in neurodegenerative disease diagnosis: from conventional techniques to soft nanomaterial-enabled electrochemical neural implants

D. Thirumalai, H. Son, D. Y. Kim, S. Choi, J. Kang*, H.-R. Lim*

TrAC Trends in Analytical Chemistry 198, 118782 (2026)

TrAC Trends
Anal. Chem.

2025 01 article

02

Identification of CO-binding modes in the Cu_B site of bovine cytochrome c oxidase by spatial mapping of binding energy

J. Kang+*, T. Matsuoka+, M. Tateno

FEBS J. · 10.1111/febs.70115

FEBS J.

2024 03 articles

03

Integration of Partially Observed Multimodal and Multiscale Neural Signals for Estimating a Neural Circuit Using Dynamic Causal Modeling

Jiyoung Kang, Hae-Jeong Park*

PLoS Comput. Biol. 20(12): e1012655 · 10.1371/journal.pcbi.1012655

PLoS Comp.
Biol.

04

A comparison between the Coleman homophily index and BA-homophily metric with a random network of unequal group sizes

Eun Lee*, Jiyoung Kang*

J. Korean Phys. Soc. · 10.1007/s40042-024-01013-x

J. Kor.
Phys. Soc.

05

Ensemble-based community detection for dynamic networks

Jiyoung Kang*

J. Korean Phys. Soc. · 10.1007/s40042-024-01224-2

J. Kor.
Phys. Soc.

2023 02 articles

06

Neuropharmacological computational analysis of longitudinal electroencephalograms in clozapine-treated patients with schizophrenia using hierarchical dynamic causal modeling

Jinseok Eo+, Jiyoung Kang+, Tak Youn, Hae-Jeong Park*

NeuroImage (2023) · 10.1016/j.neuroimage.2023.120161

NeuroImage

07

A Comprehensive Evaluation of Entropy-Based Directionality Estimation Method

Donghyeok Kim+, Eun Lee+, Jiyoung Kang+*

J. Korean Phys. Soc. · 10.1007/s40042-023-00903-w

J. Kor.
Phys. Soc.

2021 06 articles

08

State-dependent effective connectivity in resting-state fMRI

Hae-Jeong Park*+, Jinseok Eo+, Chongwon Pae, Junho Son, Sung Min Park, Jiyoung Kang*

Front. Neural Circuits (2021) · 10.3389/fncir.2021.719364

Front.
Neural Circ.

09

Empirical Bayes estimation of pairwise maximum entropy model for nonlinear brain state dynamics

Seok-Oh Jeong, Jiyoung Kang, Chongwon Pae, Jinseok Eo, Sung Min Park, Junho Son, Hae-Jeong Park

NeuroImage 244, 118618 (2021) · 10.1016/j.neuroimage.2021.118618

NeuroImage

10

Bayesian estimation of maximum entropy model for individualized energy landscape analysis of brain state dynamics

Jiyoung Kang+, Seok-Oh Jeong+, Chongwon Pae, Hae-Jeong Park+*

Hum. Brain Mapp. (2021) · 10.1002/hbm.25442

Hum. Brain
Mapp.

11

A computational framework for controlling the self-restorative brain based on the free energy and degeneracy principles

Hae-Jeong Park+*, Jiyoung Kang+*

Front. Comput. Neurosci. 15, 590019 (2021)

Front.
Comp. Neuro.

12

A computational framework for optimal control of a self-adjustive neural system with activity-dependent and homeostatic plasticity

Jiyoung Kang+, Jinseok Eo, Dong Myeong Lee, Hae-Jeong Park+

NeuroImage 230, 117805 (2021)

NeuroImage

13

Theoretical Analysis of the Dynamical Effects of the Amino Acid Residue Replacement in the Vicinity of the [4Fe-4S] Proximal Cluster on the O₂-Tolerance of the [NiFe]-Hydrogenases

Ryu-ichiro Terada, Jiyoung Kang, Masaru Tateno

J. Phys. Soc. Jpn. 90, 034804 (2021)

JPSJ

2020 02 articles

14

Dynamic causal modeling of hippocampal activity measured via mesoscopic voltage-sensitive dye imaging

Jiyoung Kang, Kyesam Jung, Jinseok Eo, Junho Son, Hae-Jeong Park

NeuroImage 213, 116755 (2020)

NeuroImage

15

Topoisomerase II targets DNA crossovers formed between distant homologous sites to induce chromatin opening

Mary Miyaji, Ryohei Furuta, Osamu Hosoya, Kuniaki Sano, Norikazu Hara, Ryozo Kuwano, Jiyoung Kang, Masaru Tateno, Kimiko M. Tsutsui, Ken Tsutsui

Sci. Rep. 10, 18550 (2020)

Sci. Rep.

2019 06 articles

16

Graph-theoretical analysis for energy landscape reveals the organization of state transitions in the resting-state human cerebral cortexEditor's pick

Jiyoung Kang, Chongwon Pae, Hae-Jeong Park

PLoS One 14, e0222161 (2019) · PLOS Complexity Channel editors' pick

PLoS One

17

Dynamic causal modeling for calcium imaging: Exploration of differential effective connectivity for sensory processing in a barrel cortical column

Kyesam Jung+, Jiyoung Kang+, Seungsoo Chung, Hae-Jeong Park

NeuroImage 201, 116008 (2019)

NeuroImage

18

Structural basis for specific recognition of core fucosylation in N-glycans by Pholiota squarrosa lectin (PhoSL)

Kazuhiko Yamasaki, Tomomi Kubota, Tomoko Yamasaki, Izuru Nagashima, Hiroki Shimizu, Ryu-ichiro Terada, Hiroshi Nishigami, Jiyoung Kang, Masaru Tateno, Hiroaki Tateno

Glycobiology 29, 576–587 (2019)

Glycobiology

19

Is it possible for short peptide composed of positively- and negatively-charged hydrophilic amino acid residue-clusters to form metastable hydrophobic packing?Cover image

Hiroshi Nishigami, Jiyoung Kang, Ryu-ichiro Terada, Hiori Kino, Kazuhiko Yamasaki, Masaru Tateno

Phys. Chem. Chem. Phys. 21, 9683–9693 (2019)

PCCP

20

Specific Coordination Mode and Electrostatic Ion Atmosphere Effects of Divalent Cations Regulating Spatially Crossing Configurations of DNA Duplexes

Hiroshi Nishigami, Jiyoung Kang, Kazuhiko Yamasaki, Masaru Tateno

J. Phys. Soc. Jpn. 88, 044801 (2019)

JPSJ

21

Novel Mechanism of Cl⁻-Dependent Proton Dislocation in Photosystem II (PSII): Hybrid Ab initio Quantum Mechanics/Molecular Mechanics Molecular Dynamics Simulation

Atsushi Nakamura, Jiyoung Kang, Ryu-ichiro Terada, Hiori Kino, Yasufumi Umena, Keisuke Kawakami, Jian-Ren Shen, Nobuo Kamiya, Masaru Tateno

J. Phys. Soc. Jpn. 88, 084802 (2019)

JPSJ

2018 02 articles

22

Redox-dependent conformational changes of a proximal [4Fe4S] cluster in Hyb-type [NiFe]-hydrogenase to protect the active site from O₂

Noor Dina Muhd Noor, Hiroaki Matsuura, Koji Nishikawa, Hulin Tai, Shun Hirota, Jaehyun Kim, Jiyoung Kang, Masaru Tateno, Ki-Seok Yoon, Seiji Ogo, Shintaro Kubota, Yasuhito Shomura, Yoshiki Higuchi

Chem. Commun. 54, 12385–12388 (2018)

Chem.
Commun.

23

Possible Transition from Hybrid Ribozyme/Protein Catalyst toward Protein Enzyme to Compensate for Defective Catalytic Activator

Kakeru Sakabe, Jiyoung Kang, Ryu-ichiro Terada, Hiroshi Nishigami, Masaru Tateno

J. Phys. Soc. Jpn. 87, 124801 (2018)

JPSJ

2017 06 articles

24

Ab Initio Electronic Structure Calculation of [4Fe-3S] Cluster of Hydrogenase as Dihydrogen Dissociation/Production Catalyst

Jaehyun Kim, Jiyoung Kang, Hiroshi Nishigami, Hiori Kino, Masaru Tateno

J. Phys. Soc. Jpn. 87, 034804 (2018)

JPSJ

25

Energy landscape analysis of the subcortical brain network unravels system properties beneath resting state dynamicsCover image

Jiyoung Kang, Chongwon Pae, Hae-Jeong Park

NeuroImage 149, 153–164 (2017)

NeuroImage

26

Simulated Annealing-Extended Sampling for Multicomponent Decomposition of Spectral Data of DNA Complexed with PeptideEditor's pick

Jiyoung Kang, Kazuhiko Yamasaki, Kuniaki Sano, Ken Tsutsui, Kimiko M. Tsutsui, Masaru Tateno

J. Phys. Soc. Jpn. 86, 014802 (2017) · Biomedical Advances editors' pick

JPSJ

27

Effects of a positive feedback loop upon the stability of bi-connected elementary biochemical reaction cycles

Jiyoung Kang, Masaru Tateno

J. Phys. Soc. Jpn. 86, 074802 (2017)

JPSJ

28

Electronic Structure Rearrangements in Hybrid Ribozyme/Protein Catalysis

Jiyoung Kang, Hiori Kino, Martin J. Field, Masaru Tateno

J. Phys. Soc. Jpn. 86, 044801 (2017)

JPSJ

29

Novel strategy for discrimination of transcription factor binding motifs employing mathematical neural network

Asuka Sugimoto, Jiyoung Kang, Takuya Sumi, Masaru Tateno

J. Phys. Soc. Jpn. 86, 074803 (2017)

JPSJ

30

Complex structure of cytochrome c–cytochrome c oxidase reveals a novel protein-protein interaction mode

Satoru Shimada, Kyoko Shinzawa-Itoh, Junpei Baba, Shimpei Aoe, Atsuhiro Shimada, Eiki Yamashita, Jiyoung Kang, Masaru Tateno, Shinya Yoshikawa, Tomitake Tsukihara

EMBO J. 86, 291–300 (2017)

EMBO J.

2013 02 articles

31

Effective Pumping Proton Collection Facilitated by a Copper Site (Cu_B) of Bovine Heart Cytochrome c Oxidase, Revealed by a Newly Developed Time-resolved Infrared System

Minoru Kubo, Satoru Nakashima, Satoru Yamaguchi, Takashi Ogura, Masao Mochizuki, Jiyoung Kang, Masaru Tateno, Kyoko Shinzawa-Itoh, Koji Kato, Shinya Yoshikawa

J. Biol. Chem. 228, 30259–30269 (2013)

JBC

32

Molecular Dynamics Study on Binding Free Energy of Azurin–Cytochrome c₅₅₁ Complex

Hiroaki Saito, Masashi Iwayama, Taku Mizukami, Jiyoung Kang, Masaru Tateno, Hidemi Nagao

Chem. Phys. Lett. 556, 297–302 (2013)

Chem. Phys.
Lett.

2012 03 articles

33

A novel ab initio identification system of transcriptional regulation motifs in genome DNA sequences based on direct comparison scheme of signal/noise distributions

Ryo Nakaki, Jiyoung Kang, Masaru Tateno

Nucleic Acids Res. 40, 8835–8848 (2012)

Nucleic
Acids Res.

34

Unidirectional mechanistic valved mechanisms for ammonia transport in GatCAB

Jiyoung Kang, Shigehide Kuroyanagi, Tomohiro Akisada, Yohsuke Hagiwara, Masaru Tateno

J. Chem. Theory Comput. 8, 649–660 (2012)

JCTC

35

Biological applications of hybrid quantum mechanics / molecular mechanics calculationReview

Jiyoung Kang, Yohsuke Hagiwara, Masaru Tateno

J. Biomed. Biotechnol. 2012, 236157 (2012)

J. Biomed.
Biotechnol.

2011 03 articles

36

A theoretical investigation of the functional role of the axial methionine ligand of the Cu_A site in cytochrome c oxidase

Jiyoung Kang, Hiori Kino, Masaru Tateno

Biochim. Biophys. Acta Bioenerg. 1807, 1314–1327 (2011)

BBA
Bioenerg.

37

Structural Instability of the Active Site of T1 Lipase Induced by Replacement of Na⁺ with Water Complexed with the Phenylalanine Aromatic Ring

Yohsuke Hagiwara, Jiyoung Kang, Masaru Tateno

J. Chem. Theory Comput. 7, 2593–2599 (2011)

JCTC

38

Japanese review article — Molecular-simulation approaches to biological macromolecules

M. Tateno, J. Kang, et al. (in Japanese)

Kotai Butsuri (Solid State Physics) 80(7), 610–614 (2011)

Solid State
Phys. (JP)

2009 02 articles

39

Electronic and geometric structures of the blue copper site of azurin investigated by QM/MM hybrid calculations

Jiyoung Kang, Takehiro Ohta, Yohsuke Hagiwara, Keigo Nishikawa, Tetsunori Yamamoto, Hidemi Nagao, Masaru Tateno

J. Phys. Condens. Matter 21, 064235 (2009)

J. Phys.
Cond. Matt.

40

A First-Principle Exploration of Heme a and Heme a₃ of the Bovine Cytochrome c Oxidase in Reduced and Oxidized Charge States

Mauro Boero, Jiyoung Kang, Shin Tokumoto, Masaru Tateno

J. Comp. Theor. Nanosci. 6, 2640–2647 (2009) · plus companion article by Ohta et al., 6, 2648–2655 (2009)

JCTN

Book chapters

Recent Progresses in Ab Initio Electronic Structure Calculation toward Understandings of Functional Mechanisms of Biological Macromolecular Systems

Use of Simulated Annealing for Biophysical Analyses of Biological Macromolecular Systems

Recent Applications of Hybrid Ab Initio Quantum Mechanics / Molecular Mechanics Simulations to Biological Macromolecules

Japanese book chapter — Molecular simulation of biological macromolecules (III: Quantum mechanics / molecular mechanics)

Patents

Method and apparatus for individualized energy-landscape analysis of brain state dynamics (Korean patent application)

Additional Korean patent application (details on file)