Yi Qin Gao (Yiqin Gao)

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 46

Top Topics

Molecular Dynamics Simulations

Transcription Factor

Top Venues

Journal of chemical theory and computation

The journal of physical chemistry letters

The journal of physical chemistry. B

The Journal of chemical physics

This page only lists publications with an associated author ORCID identifier.

Publications

Jiachen Wei, Yue Xue, Yawei Liu, Hao Tian, Yingfeng Shao, Yi Qin Gao
Steric repulsion introduced by loop constraints modulates the microphase separation of chromatins. The Journal of chemical physics 160 (5) (2024)
Xiaodong Jing, Zhen Zhu, Shuo Wang, Jiaqi Xin, Haisen Zhou, Letian Wang, Huimin Tong, Chenhui Cui, Yanfeng Zhang, Fei Sun, Lijiang Yang, Yi Qin Gao, Hua Lu
Nonionic Water-Soluble Oligo(ethylene glycol)-Modified Polypeptides with a β-Sheet Conformation. Biomacromolecules 25 (8) (2024)
Sihao Yuan, Xu Han, Jun Zhang, Zhaoxin Xie, Cheng Fan, Yunlong Xiao, Yi Qin Gao, Yi Isaac Yang
Generating High-Precision Force Fields for Molecular Dynamics Simulations to Study Chemical Reaction Mechanisms Using Molecular Configuration Transformer. The journal of physical chemistry. A (2024)
Yu-Peng Huang, Yijie Xia, Lijiang Yang, Yi Qin Gao
PMC-IZ: A Simple Algorithm for the Electrostatics Calculation in Slab Geometric Molecular Dynamics Simulations. Journal of chemical theory and computation (2024)
Yu-Peng Huang, Yijie Xia, Lijiang Yang, Yi Qin Gao
PMC-IZ: A Simple Algorithm for the Electrostatics Calculation in Slab Geometric Molecular Dynamics Simulations. Journal of chemical theory and computation 20 (2) (2024)
Xiaodong Jing, Zhen Zhu, Shuo Wang, Jiaqi Xin, Haisen Zhou, Letian Wang, Huimin Tong, Chenhui Cui, Yanfeng Zhang, Fei Sun, Lijiang Yang, Yi Qin Gao, Hua Lu
Nonionic Water-Soluble Oligo(ethylene glycol)-Modified Polypeptides with a β-Sheet Conformation. Biomacromolecules (2024)
Sihao Yuan, Xu Han, Jun Zhang, Zhaoxin Xie, Cheng Fan, Yunlong Xiao, Yi Qin Gao, Yi Isaac Yang
Generating High-Precision Force Fields for Molecular Dynamics Simulations to Study Chemical Reaction Mechanisms Using Molecular Configuration Transformer. The journal of physical chemistry. A 128 (21) (2024)
Piya Patra, Yi Qin Gao
Structural and dynamical aspect of DNA motif sequence specific binding of AP-1 transcription factor. The Journal of chemical physics 160 (11) (2024)
Jun Zhang, Dechin Chen, Yijie Xia, Yu-Peng Huang, Xiaohan Lin, Xu Han, Ningxi Ni, Zidong Wang, Fan Yu, Lijiang Yang, Yi Isaac Yang, Yi Qin Gao
Artificial Intelligence Enhanced Molecular Simulations. Journal of chemical theory and computation (2023)
Kaiyue Zhao, Hao Yu, Haocheng Xiong, Qi Lu, Yi Qin Gao, Bingjun Xu
Action at a distance: organic cation induced long range organization of interfacial water enhances hydrogen evolution and oxidation kinetics. Chemical science 14 (40) (2023)
Hao Li, Zhichen Pu, Qiming Sun, Yi Qin Gao, Yunlong Xiao
Noncollinear and Spin-Flip TDDFT in Multicollinear Approach. Journal of chemical theory and computation (2023)
Ye Tian, Yizhi Song, Yijie Xia, Jiani Hong, Yu-Peng Huang, Runze Ma, Sifan You, Dong Guan, Duanyun Cao, Mengze Zhao, Ji Chen, Chen Song, Kai-Hui Liu, Li-Mei Xu, Yi Qin Gao, En-Ge Wang, Ying Jiang
Nanoscale one-dimensional close packing of interfacial alkali ions driven by water-mediated attraction. Nature nanotechnology (2023)
Jun Zhang, Sirui Liu, Mengyun Chen, Haotian Chu, Min Wang, Zidong Wang, Jialiang Yu, Ningxi Ni, Fan Yu, Dechin Chen, Yi Isaac Yang, Boxin Xue, Lijiang Yang, Yuan Liu, Yi Qin Gao
Unsupervisedly Prompting AlphaFold2 for Accurate Few-Shot Protein Structure Prediction. Journal of chemical theory and computation (2023)
Dejia Liu, Hong Zhang, Yu-Peng Huang, Yi Qin Gao
Investigating the Activation Mechanism Differences between Human and Mouse cGAS by Molecular Dynamics Simulations. The journal of physical chemistry. B (2023)
Hao Li, Zhichen Pu, Qiming Sun, Yi Qin Gao, Yunlong Xiao
Noncollinear and Spin-Flip TDDFT in Multicollinear Approach. Journal of chemical theory and computation (2023)
Yu-Peng Huang, Hong Zhang, Siyuan Jiang, Dajiong Yue, Xiaohan Lin, Jun Zhang, Yi Qin Gao
DSDP: A Blind Docking Strategy Accelerated by GPUs. Journal of chemical information and modeling (2023)
Piya Patra, Yi Qin Gao
Sequence-Specific Structural Features and Solvation Properties of Transcription Factor Binding DNA Motifs: Insights from Molecular Dynamics Simulation. The journal of physical chemistry. B 126 (45) (2022)
Manas Mondal, Yi Qin Gao
Microscopic Insight into pH-Dependent Conformational Dynamics and Noncanonical Base Pairing in Telomeric i-Motif DNA. The journal of physical chemistry letters (2022)
Maodong Li, Jun Zhang, Haiyang Niu, Yao-Kun Lei, Xu Han, Lijiang Yang, Zhi-Qiang Ye, Yi Isaac Yang, Yi Qin Gao
Phase Transition between Crystalline Variants of Ordinary Ice. The journal of physical chemistry letters 13 (36) (2022)
Xu Han, Jun Zhang, Yi Isaac Yang, Zhen Zhang, Lijiang Yang, Yi Qin Gao
Enhanced Sampling Simulation Reveals How Solvent Influences Chirogenesis of the Intra-Molecular Diels-Alder Reaction. Journal of chemical theory and computation 18 (7) (2022)
Wenjing Zhao, Hongxu Du, Yijie Xia, Siyu Xie, Yu-Peng Huang, Tie-Qi Xu, Jie Zhang, Yi Qin Gao, Xinhua Wan
Accelerating supramolecular aggregation by molecular sliding. Physical chemistry chemical physics : PCCP 24 (38) (2022)
Yao-Kun Lei, Zhen Zhang, Xu Han, Yi Isaac Yang, Jun Zhang, Yi Qin Gao
Locating Transition Zone in Phase Space. Journal of chemical theory and computation 18 (10) (2022)
Hong Zhang, Qin Yuan Huo, Yi Qin Gao
DNA Sequence-Dependent Binding of Linker Histone gH1 Regulates Nucleosome Conformations. The journal of physical chemistry. B 126 (36) (2022)
Hao Tian, Yueying He, Yue Xue, Yi Qin Gao
Expression regulation of genes is linked to their CpG density distributions around transcription start sites. Life science alliance 5 (9) (2022)
Jun Zhang, Yao-Kun Lei, Yi Isaac Yang, Yi Qin Gao
Deep learning for variational multiscale molecular modeling. The Journal of chemical physics 153 (17) (2021)
Zhicheng Cai, Yueying He, Sirui Liu, Yue Xue, Hui Quan, Ling Zhang, Yi Qin Gao
Hierarchical dinucleotide distribution in genome along evolution and its effect on chromatin packing. Life science alliance 4 (8) (2021)
Zhi-You Wei, Li-Jiang Yang, Shi-Yan Gong, Hong-Guang Xu, Xi-Ling Xu, Yi Qin Gao, Wei-Jun Zheng
Comparison of the Microsolvation of CaX2 (X = F, Cl, Br, I) in Water: Size-Selected Anion Photoelectron Spectroscopy and Theoretical Calculations. The journal of physical chemistry. A 125 (16) (2021)
Rui Zhou, Yi Qin Gao
Polymer models for the mechanisms of chromatin 3D folding: review and perspective. Physical chemistry chemical physics : PCCP 22 (36) (2021)
Manas Mondal, Lijiang Yang, Zhicheng Cai, Piya Patra, Yi Qin Gao
A perspective on the molecular simulation of DNA from structural and functional aspects. Chemical science 12 (15) (2021)
Yue Xue, Ying Yang, Hao Tian, Hui Quan, Sirui Liu, Ling Zhang, Lu Yang, Haichuan Zhu, Hong Wu, Yi Qin Gao
Computational characterization of domain-segregated 3D chromatin structure and segmented DNA methylation status in carcinogenesis. Molecular oncology (2021)
Jiachen Wei, Hao Tian, Rui Zhou, Yingfeng Shao, Fan Song, Yi Qin Gao
Topological Constraints with Optimal Length Promote the Formation of Chromosomal Territories at Weakened Degree of Phase Separation. The journal of physical chemistry. B 125 (32) (2021)
Menghao Liu, Jun Zhang, Chenxu Zhu, Xiaoxue Zhang, Weide Xiao, Yongchang Yan, Lulu Liu, Hu Zeng, Yi Qin Gao, Chengqi Yi
DNA repair glycosylase hNEIL1 triages damaged bases via competing interaction modes. Nature communications 12 (1) (2021)
Jun Zhang, Yao-Kun Lei, Zhen Zhang, Junhan Chang, Maodong Li, Xu Han, Lijiang Yang, Yi Isaac Yang, Yi Qin Gao
A Perspective on Deep Learning for Molecular Modeling and Simulations. The journal of physical chemistry. A 124 (34) (2020)
Jin-Hu Dou, Zhi-Ao Yu, Jun Zhang, Yu-Qing Zheng, Ze-Fan Yao, Zeyi Tu, Xinchang Wang, Shiliang Huang, Chengwen Liu, Junliang Sun, Yuan-Ping Yi, Haoliang Liu, Yi Qin Gao, Jie-Yu Wang, Jian Pei
Organic Semiconducting Alloys with Tunable Energy Levels. Journal of the American Chemical Society 141 (16) (2019)
Zhuoran Qiao, Yuheng Zhao, Yi Qin Gao
Ice Nucleation of Confined Monolayer Water Conforms to Classical Nucleation Theory. The journal of physical chemistry letters 10 (11) (2019)
Yao Kun Lei, Jun Zhang, Zhen Zhang, Yi Qin Gao
Dynamic Electric Field Complicates Chemical Reactions in Solutions. The journal of physical chemistry letters 10 (11) (2019)
Jun Zhang, Yao-Kun Lei, Xing Che, Zhen Zhang, Yi Isaac Yang, Yi Qin Gao
Deep Representation Learning for Complex Free-Energy Landscapes. The journal of physical chemistry letters 10 (18) (2019)
Xiaoxia Cai, Wen Jun Xie, Ying Yang, Zhuoran Long, Jun Zhang, Zhuoran Qiao, Lijiang Yang, Yi Qin Gao
Structure of water confined between two parallel graphene plates. The Journal of chemical physics 150 (12) (2019)
Wesley Wei Wang, Maria Angulo-Ibanez, Jie Lyu, Yadagiri Kurra, Zhen Tong, Bo Wu, Ling Zhang, Vangmayee Sharma, Jennifer Zhou, Hening Lin, Yi Qin Gao, Wei Li, Katrin F Chua, Wenshe Ray Liu
A Click Chemistry Approach Reveals the Chromatin-Dependent Histone H3K36 Deacylase Nature of SIRT7. Journal of the American Chemical Society 141 (6) (2019)
Hu Zeng, Manas Mondal, Ruyi Song, Jun Zhang, Bo Xia, Menghao Liu, Chenxu Zhu, Bo He, Yi Qin Gao, Chengqi Yi
Unnatural Cytosine Bases Recognized as Thymines by DNA Polymerases by the Formation of the Watson-Crick Geometry. Angewandte Chemie (International ed. in English) 58 (1) (2018)
Bei Ding, Lijiang Yang, Debopreeti Mukherjee, Jianxin Chen, Yi Qin Gao, Feng Gai
Microscopic Insight into the Protein Denaturation Action of Urea and Its Methyl Derivatives. The journal of physical chemistry letters 9 (11) (2018)
Xing Che, Jun Zhang, Hui Quan, Lijiang Yang, Yi Qin Gao
CDNs-STING Interaction Mechanism Investigations and Instructions on Design of CDN-Derivatives. The journal of physical chemistry. B 122 (6) (2018)
Manas Mondal, Ying Yang, Lijiang Yang, Weitao Yang, Yi Qin Gao
Role of Conformational Fluctuations of Protein toward Methylation in DNA by Cytosine-5-methyltransferase. Journal of chemical theory and computation 14 (12) (2018)
Xing Che, Xiao-Xia Du, Xiaoxia Cai, Jun Zhang, Wen Jun Xie, Zhuoran Long, Zhao-Yang Ye, Heng Zhang, Lijiang Yang, Xiao-Dong Su, Yi Qin Gao
Single Mutations Reshape the Structural Correlation Network of the DMXAA-Human STING Complex. The journal of physical chemistry. B 121 (9) (2017)
Wen Jun Xie, Luming Meng, Sirui Liu, Ling Zhang, Xiaoxia Cai, Yi Qin Gao
Structural Modeling of Chromatin Integrates Genome Features and Reveals Chromosome Folding Principle. Scientific reports 7 (1) (2017)
Ling Zhang, Chan Gu, Lijiang Yang, Fuchou Tang, Yi Qin Gao
The sequence preference of DNA methylation variation in mammalians. PloS one 12 (10) (2017)