연구성과

Publications & Research Achievements

Journals

(+equally contributed authors, *corresponding author)

2025
Kang, J.+*, Matsuoka, T+. and Tateno, M. (2025), Identification of CO-binding modes in the CuB site of bovinecytochrome c oxidase by spatial mapping of binding energy. FEBS J. https://doi.org/10.1111/febs.70115
2024
1. Jiyoung Kang and Hae-Jeong Park*, Integration of Partially Observed Multimodal and Multiscale Neural Signals for Estimating a Neural Circuit Using Dynamic Causal Modeling, PLoS Comput Biol 20(12): e1012655, https://doi.org/10.1371/journal.pcbi.1012655
2. Eun Lee*, and Jiyoung Kang*, A comparison between the Coleman homophily index and BA-homophily metric with a random network of unequal group sizes, Journal of the Korean Physical Society (2024). doi: https://doi.org/10.1007/s40042-024-01013-x
3. Jiyoung Kang*, Ensemble-based community detection for dynamic networks. J. Korean Phys. Soc.(2024). https://doi.org/10.1007/s40042-024-01224-2
2023
1. Jinseok Eo+, Jiyoung Kang+, Tak Youn, Hae-Jeong Park*, Neuropharmacological computational analysis of longitudinal electroencephalograms in clozapine-treated patients with schizophrenia using hierarchical dynamic causal modeling, NeuroImage (2023), doi:https://doi.org/10.1016/j.neuroimage.2023.120161
2. Donghyeok Kim+, Eun Lee+, and Jiyoung Kang+*, A Comprehensive Evaluation of Entropy-Based Directionality Estimation Method, Journal of the Korean Physical Society (2023) https://doi.org/10.1007/s40042-023-00903-w.
2021
1. Hae-Jeong Park*+, Jinseok Eo+, Chongwon Pae, Junho Son, Sung Min Park, and Jiyoung Kang*, State-dependent effective connectivity in resting-state fMRI, Front. Neural Circuits. 2021, doi: 10.3389/fncir.2021.719364
2. Seok-Oh Jeong, Jiyoung Kang, Chongwon Pae, Jinseok Eo, Sung Min Park, Junho Son, and Hae-Jeong Park, Empirical Bayes estimation of pairwise maximum entropy model for nonlinear brain state dynamics, Neuroimage, 244, 118618, 2021. doi: 10.1016/j.neuroimage.2021.118618
3. Jiyoung Kang+, Seok-Oh Jeong+, Chongwon Pae, and Hae-Jeong Park+*, Bayesian estimation of maximum entropy model for individualized energy landscape analysis of brain state dynamics. Hum Brain Mapp. 2021. doi: 10.1002/hbm.25442.
4. Hae-Jeong Park+* and Jiyoung Kang+*, A computational framework for controlling the self-restorative brain based on the free energy and degeneracy principles, Front Comput Neurosci, 15, 590019, 2021. doi: 10.3389/fncom.2021.590019
5. Jiyoung Kang+, Jinseok Eo, Dong Myeong Lee, and Hae-Jeong Park+, A computational framework for optimal control of a self-adjustive neural system with activity-dependent and homeostatic plasticity, Neuroimage, 230, 117805, 2021.
6. Ryu-ichiro Terada, Jiyoung Kang, Masaru Tateno, 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, J. Phys. Soc. Jpn., 90, 034804, 2021.
2020
7. Jiyoung Kang, Kyesam Jung, Jinseok Eo, Junho Son, and Hae-Jeong Park, Dynamic causal modeling of hippocampal activity measured via mesoscopic voltage-sensitive dye imaging, Neuroimage, 213, 116755, 2020.
8. Mary Miyaji, Ryohei Furuta, Osamu Hosoya, Kuniaki Sano, Norikazu Hara, Ryozo Kuwano, Jiyoung Kang, Masaru Tateno, Kimiko M. Tsutsui, and Ken Tsutsui, Topoisomerase IIβ targets DNA crossovers formed between distant homologous sites to induce chromatin opening. Sci. Rep. 10, 18550, 2020.
2019
9. Jiyoung Kang, Chongwon Pae, and Hae-Jeong Park, Graph-theoretical analysis for energy landscape reveals the organization of state transitions in the resting-state human cerebral cortex, PLoS One, 14, e0222161, 2019.
*Editor’s pick (PLOS Complexity Channel): https://channels.plos.org/complexity
10. Kyesam Jung+, Jiyoung Kang+, Seungsoo Chung, and Hae-Jeong Park, Dynamic causal modeling for calcium imaging: Exploration of differential effective connectivity for sensory processing in a barrel cortical column, Neuroimage, 201, 116008, 2019.
11. Kazuhiko Yamasaki, Tomomi Kubota, Tomoko Yamasaki, Izuru Nagashima, Hiroki Shimizu, Ryu-ichiro Terada, Hiroshi Nishigami, Jiyoung Kang, Masaru Tateno, Hiroaki Tateno, Structural basis for specific recognition of core fucosylation in N-glycans by Pholiota squarrosa lectin (PhoSL), Glycobiology, 29, 576–587, 2019.
12. Hiroshi Nishigami, Jiyoung Kang, Ryu-ichiro Terada, Hiori Kino, Kazuhiko Yamasaki, Masaru Tateno, Is it possible for short peptide composed of positively- and negatively-charged “hydrophilic” amino acid residue-clusters to form metastable “hydrophobic” packing?, Physical Chemistry Chemical Physics, 21, 9683-9693, 2019. (Cover Image)
13. Hiroshi Nishigami, Jiyoung Kang, Kazuhiko Yamasaki, and Masaru Tateno, Specific Coordination Mode and Electrostatic Ion Atmosphere Effects of Divalent Cations Regulating Spatially Crossing Configurations of DNA Duplexes, J. Phys. Soc. Jpn., 88, 044801, 2019.
14. Atsushi Nakamura, Jiyoung Kang, Ryu-ichiro Terada, Hiori Kino, Yasufumi Umena, Keisuke Kawakami, Jian-Ren Shen, Nobuo Kamiya, Masaru Tateno, Novel Mechanism of Cl-Dependent Proton Dislocation in Photosystem II (PSII): Hybrid Ab initio Quantum Mechanics/Molecular Mechanics Molecular Dynamics Simulation, J. Phys. Soc. Jpn., 88, 084802, 2019.
2018
15. 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, and Yoshiki Higuchi, Redox-dependent conformational changes of a proximal [4Fe–4S] cluster in Hyb-type [NiFe]-hydrogenase to protect the active site from O2, Chem. Comm., 54, 12385-12388, 2018.
16. Kakeru Sakabe, Jiyoung Kang, Ryu-ichiro Terada, Hiroshi Nishigami, and Masaru Tateno, Possible Transition from Hybrid Ribozyme/Protein Catalyst toward Protein Enzyme to Compensate for Defective Catalytic Activator, J. Phys. Soc. Jpn., 87, 124801, 2018.
17. Jaehyun Kim, Jiyoung Kang, Hiroshi Nishigami, Hiori Kino, and Tateno, Masaru, Ab Initio Electronic Structure Calculation of [4Fe-3S] Cluster of Hydrogenase as Dihydrogen Dissociation/Production Catalyst, J. Phys. Soc. Jpn., 87, 034804, 2018.
2017
18. Jiyoung Kang, Chongwon Pae, and Hae-Jeong Park, Energy landscape analysis of the subcortical brain network unravels system properties beneath resting state dynamics, Neuroimage, 149, 153–164, 2017. (Cover Image)
19. Jiyoung Kang, Kazuhiko Yamasaki, Kuniaki Sano, Ken Tsutsui, Kimiko M. Tsutsui, and Masaru Tateno, Simulated Annealing-Extended Sampling for Multicomponent Decomposition of Spectral Data of DNA Complexed with Peptide, J. Phys. Soc. Jpn., 86, 014802, 2017.
*Editor’s pick (Biomedical Advances): http://biomedical-advances.org/ep-20179-5/
20. Jiyoung Kang and Masaru Tateno, Effects of a positive feedback loop upon the stability of bi-connected elementary biochemical reaction cycles, J. Phys. Soc. Jpn, 86, 074802, 2017.
21. Jiyoung Kang, Hiori Kino, Martin J. Field, and Masaru Tateno: Electronic Structure Rearrangements in Hybrid Ribozyme/Protein Catalysis, J. Phys. Soc. Jpn., 86, 044801, 2017.
22. Asuka Sugimoto, Jiyoung Kang, Takuya Sumi, and Masaru Tateno, Novel strategy for discrimination of transcription factor binding motifs employing mathematical neural network, J. Phys. Soc. Jpn., 86, 074803, 2017.
23. Satoru Shimada, Kyoko Shinzawa-Itoh, Junpei Baba, Shimpei Aoe, Atsuhiro Shimada, Eiki Yamashita, Jiyoung Kang, Masaru Tateno, Shinya Yoshikawa and Tomitake Tsukihara, Complex structure of cytochrome c-cytochrome c oxidase reveals a novel protein-protein interaction mode, EMBO J., 86, 291-300, 2017.
2013
24. Minoru Kubo, Satoru Nakashima, Satoru Yamaguchi, Takashi Ogura, Masao Mochizuki, Jiyoung Kang, Masaru Tateno, Kyoko Shinzawa-Itoh, Koji Kato, and Shinya Yoshikawa, Effective Pumping Proton Collection Facilitated by a Copper Site (CuB) of Bovine Heart Cytochrome c Oxidase, Revealed by a Newly Developed Time-resolved Infrared System: J. Biol. Chem., 228, 30259-69, 2013.
25. Hiroaki Saito, Masashi Iwayama, Taku Mizukami, Jiyoung Kang, Masaru Tateno, Hidemi Nagao, Molecular Dynamics Study on Binding Free Energy of Azurin–Cytochrome c551 Complex, Chem. Phys. Lett., 556, 297–302, 2013.
2012
26. Ryo Nakaki, Jiyoung Kang, and Masaru Tateno, A novel ab initio identification system of transcriptional regulation motifs in genome DNA sequences based on direct comparison scheme of signal/noise distributions: Nucleic Acids Res., 40, 8835-48, 2012.
27. Jiyoung Kang, Shigehide Kuroyanagi, Tomohiro Akisada, Yohsuke Hagiwara, and Masaru Tateno, Unidirectional mechanistic valved mechanisms for ammonia transport in GatCAB: J. Chem. Theory Comput., 8, 649-660, 2012.
28. Jiyoung Kang, Yohsuke Hagiwara, and Masaru Tateno, Biological applications of hybrid quantum mechanics / molecular mechanics calculation, J. Biomed. Biotech., 2012, 236157, 2012, http://dx.doi.org/10.1155/2012/236157 (Review article)
2011
29. Jiyoung Kang, Hiori Kino, and Masaru Tateno, A theoretical investigation of the functional role of the axial methionine ligand of the CuA site in cytochrome c oxidase, Biochim. Biophys. Acta Bioenerg., 1807, 1314-27, 2011.
30. Yohsuke Hagiwara, Jiyoung Kang, and Masaru Tateno, Structural Instability of the Active Site of T1 Lipase Induced by Replacement of Na+ with Water Complexed with the Phenylalanine Aromatic Ring, J. Chem. Theory. Comput., 7, 2593-99, 2011.
34. 姜 志姈，萩原陽介，舘野　賢, コンピュータ・シミュレーションによる生体触媒反応機構の研究, 応用物理(2011), 第80券, 第7号, p.610 –14, 2011. (Japanese review article, 컴퓨터 시뮬레이션에 의한 생체촉매반응매커니즘의 연구, 응용물리)
2009
31. Jiyoung Kang, Takehiro Ohta, Yohsuke Hagiwara, Keigo Nishikawa, Tetsunori Yamamoto, Hidemi Nagao, and Masaru Tateno: Electronic and geometric structures of the blue copper site of azurin investigated by QM/MM hybrid calculations: J. Phys. Cond. Matt., 21, 064235, 2009.
32. Mauro Boero, Jiyoung Kang, Shin Tokumoto, and Masaru Tateno: A First-Principle Exploration of Heme a and Heme a3 of the Bovine Cytochrome c Oxidase in Reduced and Oxidized Charge States: J. Comp. Theor. Nanosci., 6, 2640-47, 2009.
33. Takehiro Ohta, Yohsuke Hagiwara, Jiyoung Kang, Keigo Nishikawa, Tetsunori Yamamoto, Hidemi Nagao, and Masaru Tateno: Evaluation of Electronic and Geometrical Properties of the Blue Copper Site in Fully Solvated Azurin by QM/MM Hybrid Calculations Using a New Interface Program Connecting QM and MM Engine: J. Comp. Theor. Nanosci., 6, 2648-55, 2009.

Books

Book Chapter

1. Jiyoung Kang, Takuya Sumi and Masaru Tateno, Recent Progresses in Ab Initio Electronic Structure Calculation toward Understandings of Functional Mechanisms of Biological Macromolecular Systems, “Panorama of Contemporary Quantum Mechanics - Concepts and Applications”, edited by Trong Tuong Truong, 2019, IntechOpen, DOI: 10.5772/intechopen.83545
2. Jiyoung Kang, Takuya Sumi, Hiroshi Yamaguchi and Masaru Tateno, Use of Simulated Annealing for Biophysical Analyses of Biological Macromolecular Systems, “Simulated Annealing; Introduction, Applications and Theory”, book edited by Alex Scollen and Thomas Hargraves, 49-84, 2018, ISBN: 978-1-53613-674-6.
3. Jiyoung Kang and Masaru Tateno, Recent Applications of Hybrid Ab Initio Quantum Mechanics / Molecular Mechanics Simulations to Biological Macro- molecules, “Some Applications of Quantum Mechanics", book edited by Mohammad Reza Pahlavani, DOI: 10.5772/35092, 2012, ISBN: 978-953-51-0059-1.

Japanese book chapter

4. 萩原陽介，姜 志姈，舘野　賢, 生体反応の量子ハイブリッド分子動力学シミュレーション, 赤井久純，白井光雲編　「密度汎関数理論の発展とマテリアルデザインへの応用」シュプリンガージャパン, 第III部/第８章, 2011. (Japanese Book) 생체반응의 양자하이브리드 분자동역학 시뮬레이션, 밀도범함수이론의 발전과 재료디자인으로의 응용, 스프링거-재팬, 제3부, 8장

Patent

1) 베이지안 최대엔트로피모델 추정 및 뇌 기능 동적 특성 평가 방법, 특허 출원, 연세대 산학협력단, 한국외국어 대학교 산학협력단, 발명자: 박해정, 강지영, 정석오, 출원등록일: 2019. 10. 11, 출원등록번호: 10-2019-0126365
2) 특허 등록

Conference Presentations

2025

International Conference

• Metabolically-Informed Dynamic Causal Modeling of Ketogenic Therapy in Childhood Epilepsy, Jiyoung Kang, Euisun Kim, Hae-Jeong Park, 2025, KSBNS, (The 28 th Annual Meeting of the Korean Society for Brain and Neural Sciences, The 3rd CJK Neuroscience Meeting), 2025/8/24-2025/8/27, Songdo convensia, Incheon, Republic of Korea

• Thalamocortical Neuropharmacology in Absence Epilepsy: A Computational Model of T-type Ca²⁺ and Na⁺ Channel Dynamics, Euisun Kim, Jiyoung Kang, Jinseok Eo, Ara Ko, Joon Soo Lee, Sangbo Lee, Hae-Jeong Park, 2025, KSBNS, (The 28 th Annual Meeting of the Korean Society for Brain and Neural Sciences, The 3rd CJK Neuroscience Meeting), 2025/8/24-2025/8/27, Songdo convensia, Incheon, Republic of Korea

• Computational Modeling of Ca2+ Blocker Effect in the Thalamocortical Network of Epilepsy: A Dynamic Causal Modeling Study, Euisun Kim, Jiyoung Kang, Jinseok Eo, Hae-Jeong Park, 2025, Comuputational Neuroscience, 2025/7/5-2025/7/9, Florence, Italy

Domestic Conference

[Poster]

[Oral]

2024

International Conference

• Analysis of decision-making strategies based on previous choice in a rat gambling task, Myung Ji Kwak, Jiyoung Kang, Wha Young Kim, Jeong-Hoon Kim, 2024, KSBNS, (The 27 th Annual Meeting of the Korean Society for Brain and Neural Sciences in conjunction with the 18 th Biennial Meeting of the Asian-Pacific Society for Neurochemistry), 2024/10/15-2024/10/18, HICO, Gyeongju, Republic of Korea

• Computational modeling and analysis of TMS-induced brain dynamics patterns, Jiyoung Kang, Haejeong Lee, 2024, KSBNS, (The 27 th Annual Meeting of the Korean Society for Brain and Neural Sciences in conjunction with the 18 th Biennial Meeting of the Asian-Pacific Society for Neurochemistry), 2024/10/15-2024/10/18, HICO, Gyeongju, Republic of Korea

Domestic Conference

[Poster]

• A computational approach for multiple TMS-induced brain dynamics, Lee Haejeong , Kang Jiyoung, 2024 한국물리학회 봄학술대회, 대전 컨벤션센터, 2024/04/23-26.


[Oral]

2023

International Conference

[Poster]

• Dynamic causal modeling for multimodal and multiscale neural dynamic signals, Jiyoung Kang, Hae-Jeong Park, the Korean Society for Brain and Neural Sciences 2023, BEXCO, Busan, South Korea, 2023/09/06-2023/09/08

• Personalized grid-based whole brain dynamics modeling approach to characterize response network induced by transcranial magnetic stimulation, Sora An, Chaewon Kang, Yunjun Hwang, Donghyeok Kim, Jiyoung Kang, the Korean Society for Brain and Neural Sciences 2023, BEXCO, Busan, South Korea, 2023/09/06-2023/09/08

• Neuropharmacological computational analysis of longitudinal electroencephalograms using dynamic causal modeling, Jinseok Eo, Jiyoung Kang, Tak Youn, Hae-Jeong Park, the Korean Society for Brain and Neural Sciences 2023, BEXCO, Busan, South Korea, 2023/09/06-2023/09/08

• A systematic study of energy landscape analysis with a pairwise maximum entropy model for exploring resting state brain dynamics, Suhail Ahmad Ganie, Yunjun Hwang, Jiyoung Kang, the Korean Society for Brain and Neural Sciences 2023, BEXCO, Busan, South Korea, 2023/09/06-2023/09/08

• Changes in brain networks induced by repetitive single-pulse transcranial magnetic stimulation, Chaewon Kang, Sora An, Donghyeok Kim, Jiyoung Kang, the Korean Society for Brain and Neural Sciences 2023, BEXCO, Busan, South Korea, 2023/09/06-2023/09/08


[Oral]

• State Transition Network Analysis for Energy Landscape of Brain at Rest, Jiyoung Kang, Hae-Jeong Park, International Conference on Biological Physics 2023, Seoul, Korea , 2023/08/14-2023/08/18 (Invited talk)

Domestic Conference

[Poster]

• Investigating the the Neurobiological Basis of Pairwise Maximum Entropy Models, Haejeong Lee, Jiyoung Kang, 대한뇌기능매핑학회 2023, 수원 성균관대학교 반도체관, 2023/10/27-2023/10/28

• A Comprehensive Evaluation of Information Entropy-baseed Network Directionality Estimation Method using world trade web and brain networks, Donghyeok Kim, Eun Lee, Jiyoung Kang, 2023 한국물리학회 가을학술대회, Changwon Exhibition Convention Center, 2023/10/24-2023/10/27

• Quantifying concurrency of edges in temporal networks, Jiyoung Kang, Naoki Masuda, 2023 한국물리학회 가을학술대회, Changwon Exhibition Convention Center, 2023/10/24-2023/10/27

• Computational Approaches to Understanding and Controlling Brain Dynamics, Jiyoung Kang, StatPhys Monthly Meeting, UNIST, Ulsan & Online (ZOOM), 2023/06/16-2023/06/17


[Oral]

• Multimodal Dynamic Causal Modeling: A Novel Computational Framework for Integrating Local and Global Circuit Information in Multiscale Brain Model Construction, Jiyoung Kang, 대한뇌기능매핑학회 2023, 수원 성균관대학교 반도체관, 2023/10/27-10/28.

2022

International Conference

[Poster]

• A computational method for effective brain controls based on degeneracy and free energy principles, Neuroscience 2022, Online & Sandiego, Society for Neuroscience, USA, Jiyoung Kang and Hae-Jeong Park, 2022/11/12-11/16.

• Development of a computational framework for prediction of effective connectivity changes induced by transcranial magnetic stimulation, KSBNS 2022, Incheon, Korea, Jiyoung Kang, Sora Ahn, and Hae-Jeong Park, 2022/05/19-2022/05/21.


[Oral]

• Computational approaches for effective brain controls based on brain dynamics, RHINO 2022, Tokyo, Japan, Jiyoung Kang, 2022/09/16-2022/09/17 (Invited talk)

Domestic Conference

[Poster]

• Simulation-based optimal control of self-adjustive brain circuits, The Korean Physical Society, Jiyoung Kang and Hae-Jeong Park, 2022/10/19-10/21.

• Altered nonlinear brain state dynamics in the resting state of schizophrenia, 대한뇌기능매핑학회 KHBM2022, Jiyoung Kang and Hae-Jeong Park, 2022/11/18-11/19.

• A computational scheme for evaluating brain network changes evoked by transcranial magnetic stimulation, 대한뇌기능매핑학회 KHBM2022, Donghyeok Kim, Sora An, Hae-Jeong Park, Jiyoung Kang, 2022/11/18-11/19.


[Oral]

• 내재화 및 외현화 내적표현형 기반 심리 부적응 고위험군 선별 유형화 예비모델링을 위한 겜블링 과제 동물실험 모델 및 인간 빅데이터(HCP) 분석연구, A Preliminary Study of Screening High-risk Group for Psychological Maladaptation based on Psychological Endophenotyping of Internalizing and Externalizing Features in Human Connectome Project (HCP) and Animal Experimental Model (Rat Gambling Task), 2022 제76차 한국심리학회 연차학술대회, 서울 & 온라인, 강지영, 김화영, 최혜윤, 엄소용, 2022/08/18-2022/08/19.

2021

International Conference

[Poster]

• A computational approach for optimal control of self-adjustment brain, Jiyoung Kang, Jinseok Eo, Dong Myeong Lee, Hae-Jeong Park, OHBM 2021, June 24 (June 21-25)

• An integrative framework for dynamic causal modeling of neural circuitry using multiscale, multimodal measurements, Jiyoung Kang and Hae-Jeong Park, CNS2021, Online, 2021, July 4 (July 3- July 7)

• A computational scheme for optimal control of brain with consideration of activity-dependent and homeostatic plasticity, Jiyoung Kang, Jinseok Eo, and Hae-Jeong Park, IBEC, 2021, (Online)

Domestic Conference

[Poster]

• Bayesian estimation of pairwise maximum entropy model for brain state dynamics of individuals, Jiyoung Kang, Seok-Oh Jeong, Chongwon Pae, and Hae-Jeong Park, KSBNS, Seoul & Online, 2021, May 21 (May 20-May 21) (Online)

• A computational framework for simulating effective connectivity changes evoked by transcranial electrical stimulation (tES), Jiyoung Kang, Sora An, Sole Yoo, Jinseok Eo and Hae-Jeong Park, KHBM, 2021 (online)

• Personalized In-Silico Approach to Analyze Response Characteristics of Brain Network Evoked by Transcranial Magnetic Stimulation, Sora An, Jiyoung Kang, and Hae-Jeong Park, KHBM, 2021 (online)


[Oral]

• A control scheme for the self-restorative brain: a computational approach based on the free energy and degeneracy principles, Jiyoung Kang and Hae-Jeong Park, KSBNS, Seoul & Online, 2021, May 21 (May 20-May 21) (Selected as Best Oral Presentation)