朱通 副研究员副研究员
化学与分子工程学院??????


导航
个人资料
研究方向
开授课程
科研项目
学术成果
荣誉及奖励







个人资料
部门： 化学与分子工程学院
毕业院校： 华东师范大学
学位： 博士
学历： 研究生
邮编： 200062
联系电话：
传真：
电子邮箱： tzhu@lps.ecnu.edu.cn
办公地址： 中山北路校区理科大楼A1008a
通讯地址： 上海市中山北路3663号华东师大理科大楼A1008a

教育经历

工作经历
副研究员2015至今华东师范大学化学与分子工程学院
访问****2016-2018台湾“中央研究院” 生物医学科学研究所
博士后2014-2015华东师范大学化学与分子工程学院

个人简介
The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!
社会兼职
Biophysical Journal, ACS Omega, Scientific Reports, Journal of Computational Chemistry, RSC Advances, Molecular Simulation, Journal of Molecular Modeling, Journal ofChemical Information and Modeling, Journal ofChemical Theory and Computation, Journal of Physical Chemistry A/B, Physical Chemistry Chemical Physics, Chemical Physics Letters等杂志审稿人。


研究方向
课题组主页 (Group website)
欢迎加入本课题组！！！

课题组最新动态

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2019-07热烈祝贺曾晋哲，肖进荣获第十二届中国大学生计算机设计大赛一等奖！

2019-05祝贺赵培顺利通过硕士论文答辩！祝贺陈娱，杨颜萍，曾晋哲顺利通过本科论文答辩！
2019-04祝贺曾晋哲，肖进荣获第十一届上海市大学生计算机应用能力大赛一等奖！

2019-02恭喜陈娱和曾晋哲分别获得Rice和Rutgers大学研究生院(博士生项目)的录取通知！！
2019-02课题组开发的反应网络分析工具 ReacNetGenerator正式上线！

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主要研究方向：
金属离子与蛋白/核酸相互作用的多尺度计算模拟，包括分子力场的开发、分块量子化学计算以及增强采样；



复杂体系的反应机理研究，包括燃烧反应，非均相催化以及基于机器学习的方法开发；


计算机辅助药物设计。

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研究组成员：
徐明远
曹立群
高振梅
刘瑶
张琪
肖 进
沈 强
顾双菲（本科生）
雷琪（本科生）
黎娜（本科生）
王佳乐（本科生）

已毕业学生：
赵培(2019年硕士毕业，国家知识产权专利局)
曹华丽(2019年硕士毕业，上海市静安区实验中学)

曾晋哲(2019年本科毕业，RutgersUniversity，博士生)
陈娱(2019年本科毕业，Rice University，博士生）
杨颜萍(2019年本科毕业，龙岩中学)

如果您对我们我们的研究领域有兴趣，欢迎加入我们科研小组实习、做本科毕业设计和读研。我们将为大家提供优厚的待遇和丰富的学术交流机会。有志出国的同学可获得有效的锻炼和实事求是的推荐。


开授课程
《结构化学》本科生
《量子化学与分子模拟在化学中的应用》研究生
《人工智能与化学》本科生



科研项目
主持项目：

国家自然科学基金重大计划培育项目
NYU-ECNU seed grant
国家自然科学基金青年项目
中国博士后基金面上项目

参与项目：

国家自然科学基金重点项目
国家重点研发计划



学术成果
论文

2020

57. Z Gao, J Bao, S Shi, X Zhang, Y Gao,Zhu T.*,Effect of Mutations on Drug Resistance of Smoothened Receptor Toward Inhibitors Probed by Molecular Modeling.Chem. Phys. Lett.2020, 741, 137126.
56. Xianli Hu, Bo Hou, Zhiai Xu, Madiha Saeed, Fang Sun, Zhenmei Gao, Yi Lai,Zhu T,Fan Zhang, Wen Zhang, Haijun Yu*.Supramolecular Prodrug Nanovectors for Active Tumor Targeting and Combination Immunotherapy of Colorectal Cancer.Adv. Sci.2020, 7, **
55. Zeng, J. Z.; Cao, L. Q.; Xu, M. Y.;Zhu T.*;Zhang, J. Z. H.*, Neural Network Based in Silico Simulation of Combustion Reactions. arXiv:1911.12252.
54. Zeng, J. Z.,? Cao, L. Q., ? Chin, C. H.;* Ren, H. S.;* Zhang, J. Z. H.;Zhu T.*, ReacNetGenerator: an automatic reaction network generator for reactive molecular dynamics simulations.Phys. Chem. Chem. Phys.,2020, 22, 683-691.



2019
53. Chin, C. H.*; Zhu, T.*; Zhang, J. Z. H.,Formation mechanism and spectroscopy of C6H radicals in extreme environments: a theoretical study.Phem. Chem. Chem. Phys.,2019, 21, 23044-23055.
52. Tian, S. Z.; Zeng, J. Z.; Liu, X.*; Chen, J. Z.; Zhang, J. Z. H.;Zhu, T.*,Understanding the selectivity of inhibitors toward PI4KIIIa and PI4KIIIb based molecular modeling.Phem. Chem. Chem. Phys.,2019, 21, 22103-22112.
51. Chen, J. Z.*; Pang, L. X.; Wang, W.; Wang, L. F.; Zhang, J. Z. H.;Zhu T.*,Binding modes and conformational changes of FK506-binding protein 51 induced by inhibitor bindings: insight into molecular mechanisms based on multiple simulation technologies.J. Biomol. Struct. Dyn.,2019, 21, 22103-22112.J. Biomol. Struct. Dyn., 2019, DOI: 10.1080/**.2019.**.
50. Xu, M.Y.;Zhu, T.*; Zhang J. Z. H.*,Molecular Dynamics Simulation of Zinc Ion in Water with an Ab Initio Based Neural Network Potential.J. Phys. Chem. A,2019, 123, 6587-6595.

49.Tang, Q.; Plank, T. N.;Zhu, T.; Yu H. Z.; Ge Z. L.; Li Q.; Li L.; Davis J. T.*; Pei H.*,Self-Assembly of Metallo-Nucleoside Hydrogels for Injectable Materials That Promote Wound Closure. ACS Appl. Mater.Interfaces.2019, 11, 19743?19750
48. Zhao, P.; Han, S.; Li, X. X.*; Zhu, T.*; Tao, X. F.; Guo, L., Comparison of RP-3 Pyrolysis Reactions Between Surrogates and 45-component Model by ReaxFF MD Simulations.ACSEnergy Fuels.,2019, 33, 7176-7187.
47. Sun, Z. X.*; Wang, X. H.; Zhao, Q. Q.;Zhu, T.,Understanding Aldose Reductase-Inhibitors interactions with free energy simulation.J. Mol. Graph. Model.,2019, 91, 10-21.
46. Chen, J. Z.*; Wang, X. Y.; Pang, L. X.; Zhang, J. Z. H.;Zhu, T.*, Effect of mutations on binding of ligands to guanine riboswitch probed by free energy perturbation and molecular dynamics simulations.Nucleic Acids Res.,2019, 47,6618-6631.
45. Zhao, P.; Cao, H. L.; Chen, Y.;Zhu, T.*, Insights into the binding mechanisms of inhibitors of MDM2 based on molecular dynamics simulations and binding free energy calculations.Chem. Phys. Lett., 2019, 728, 94-101.
44. Chen, J. Z.*; Pang, L. X.; Wang, W.; Wang, L. F.; Zhang, J. Z. H.;Zhu, T.*, Decoding molecular mechanism of inhibitor bindings to CDK2 using molecular dynamics simulations andbinding free energy calculations.J. Biomol. Struct. Dyn., 2019, 8, 1-12.
43. Zhu, M. F.; Wang, H.; Wang, C. L.; Fang, Y. F.; Zhu, T.;Zhao, W. L.; Dong, X. C.*; Zhang, X. W.*, L-4, a Well-Tolerated and Orally Active Inhibitor of Hedgehog Pathway, Exhibited Potent Anti-tumor Effects Against Medulloblastoma in vitro and in vivo. Front. Pharm.,2019, 10, 1-13.
42. Xu, M. Y.;Zhu, T.*; Zhang, J. Z. H.*, A Fragment Quantum Mechanical Method for Metalloproteins.J. Chem. Theory Comput.,2019, 15, 1430–1439.

2018
41. Chen, J. Z.*; Wang, X. Y.; Zhang, J. Z. H.;Zhu, T.*,Effect of Substituents in Different Positions of Aminothiazole Hinge-Binding Scaffolds on Inhibitor–CDK2 Association Probed by Interaction Entropy Method.ACS Omega, 2018, 3, 18052–18064.
40. Gao, Y.;Zhu, T.*; Zhang, C. M.; Zhang, J. Z. H.; Mei, Y.*,Comparison of the Unfolding and Oligomerization of Human Prion Protein under acidic and neutral environments by Molecular Dynamics Simulations.Chem. Phys. Lett.,2018, 706, 594-600.
39. Gao, Y.;Zhu, T.*; Chen, J. Z.*,Exploring Drug-resistant Mechanisms of I84V Mutation in HIV-1 Protease toward Different Inhibitors by Thermodynamics Integration and Solvated Interaction Energy Method. Chem. Phys. Lett.,2018, 706, 400-408.
38. Yang, Q.; Hu, Z.; Zhu, S.; Ma, R.; Ma, H.; Ma, Z.; Wan, H.; Zhu, T.;Jiang, Z.; Liu, W.; Jiao, L.; Sun, H. T.*; Liang, Y. Y.*; Dai, H. J.*, Donor Engineering for NIR-II Molecular Fluorophores with Enhanced Fluorescent Performance. J. Am. Chem. Soc.2018, 140, 1715-1724.
37. Xu, M.;Zhu, T.*;Zhang, J. Z. H.*, A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein.Front. Chem.,2018, 6, 189.
36. Wang, X. W.*; Li, Y.; Gao, Y.; Yang, Z.; Lu, C.;Zhu, T.*,A quantum mechanical computational method for modeling electrostatic and solvation effects of protein. Sci. Rep.2018, 8, 5475.
35. Jin, X.;Zhu, T.; Zhang, J. Z. H.; He, X.*, Automated Fragmentation QM/MM Calculation of NMR Chemical Shifts for Protein-Ligand Complexes. Front. Chem.,2018, 6, 150.


2017
34. Xi, J. B.; Fang, Y.-F.; Frett, B.; Zhu, M. L.;Zhu, T.;Kong, Y.-N.; Guan, F.-J.; Zhao, Y.; Zhang, X. W.*; Li, H. Y.*; Ma, M. L.*; Hu, W. H.*, Structure-based design and synthesis of imidazo 1,2-a pyridine derivatives as novel and potent Nek2 inhibitors with in vitro and in vivo antitumor activities. Eur. J.Med. Chem.,2017, 126, 1083-1106.
33. Sun, Z. X.*;Zhu, T.;Wang, X. H.; Mei, Y.; Zhang, J. Z. H.*, Optimization of convergence criteria for fragmentation methods.Chem. Phys. Lett.,2017, 687, 163-170.
32. Luo, Z. J.; Gao, Y.;Zhu, T.*;Zhang, J. Z.; Xia, F.*, Origins of Protons in C-H Bond Insertion Products of Phenols: Proton-Self-Sufficient Function via Water Molecules.J. Phys. Chem. A,2017, 121, 6523-6529.
31. Liu, L.; Zhao, F.; Liu, W.;Zhu, T.; Zhang, J. Z. H.; Chen, C.; Dai, Z.; Peng, H.; Huang, J. L.; Hu, Q.; Bu, W.; Tian, Y.*, An Electrochemical Biosensor with Dual Signal Outputs: Toward Simultaneous Quantification of pH and O-2 in the Brain upon Ischemia and in a Tumor during Cancer Starvation Therapy. Angew. Chem. Int.Edit.,2017, 56, 10471-10475.
30. Li, S.; Zhu, A. W.*;Zhu, T.;Zhang, J. Z. H.; Tian, Y.*, Single Biosensor for Simultaneous Quantification of Glucose and pH in a Rat Brain of Diabetic Model Using Both Current and Potential Outputs. Anal. Chem.,2017, 89, 6656-6662.
29. Jing, C.; Li, Z.; Jia, K.; Chen, C.; Liu, X.; Wang, B.; Hu, W.; Li, J.;Zhu, T*.; Dong, S.*, Discovery of Bisindole as a Novel Scaffold for Protein Tyrosine Phosphatase 1B Inhibitors. Arch. Pharm.,2017, 350, e**.
28. Huang, M. M.; Luo, Z. J.;Zhu, T.; Chen, J.*; Zhang, J. Z.; Xia, F.*, A theoretical study of the substituent effect on reactions of amines, carbon dioxide and ethylene oxide catalyzed by binary ionic liquids. RSCAdv.,2017, 7, 51521-51527.
27. Gao, Y.*; Zhang, C. M.; Wang, X. W.;Zhu, T.*,A test of AMBER force fields in predicting the secondary structure of alpha-helical and beta-hairpin peptides.Chem. Phys. Lett.,2017, 679, 112-118.
26. Duan, L. L.*;Zhu, T.; Li, Y. C.; Zhang, Q. G.; Zhang, J. Z. H.*, Effect of polarization on HIV-1protease and fluoro-substituted inhibitors binding energies by large scale molecular dynamics simulations. Sci. Rep.,2017, 7, 42223.
25. Duan, L.;Zhu, T.;Ji, C. G.; Zhang, Q. G.; Zhang, J. Z. H.*, Direct folding simulation of helical proteins using an effective polarizable bond force field. Phys. Chem. Chem. Phys.,2017, 19, 15273-15284.
24. Dong, S. Z.*; Lei, Y. B.*; Jia, S.*; Gao, L. X.*; Li, J.*;Zhu, T.*; Liu, S. Y.*; Hu, W. H.*, Discovery of core-structurally novel PTP1B inhibitors with specific selectivity containing oxindole-fused spirotetrahydrofurochroman by one-pot reaction. Bioorg. Med. Chem. Lett.,2017, 27, 1105-1108.


2016
23. Wang, Y.; Liu, J. F.;Zhu, T.; Zhang, L. J.; He, X.*; Zhang, J. Z. H.*, Predicted PAR1 inhibitors from multiple computational methods. Chem. Phys. Lett.,2016, 659, 295-303.
22. Lv, F.; Chen, C.; Tang, Y.; Wei, J.;Zhu, T.*; Hu, W. H.*., New peptide deformylase inhibitors design, synthesis and pharmacokinetic assessment.Bioorg. Med. Chem. Lett.,2016, 26, 3714-3718.
21. Liu, X.; Liu, J. F.;Zhu, T.;Zhang, L. J.; He, X.*; Zhang, J. Z. H.*, PBSA_E: A PBSA-Based Free Energy Estimator for Protein-Ligand Binding Affinity. J. Chem. Inf. Model.,2016, 56, 854-861.
20. Liu, W.; Lu, Y.; Chai, X.; Liu, X.;Zhu, T.;Wu, X.; Fang, Y. F.*; Liu, X.*; Zhang, X. W.*, Antitumor activity of TY-011 against gastric cancer by inhibiting Aurora A, Aurora B and VEGFR2 kinases.J. Exp. Clin. Canc. Res.,2016, 35, 183.
19. Jin, X.;Zhu, T.;Zhang, J. Z. H.; He, X.*, A systematic study on RNA NMR chemical shift calculation based on the automated fragmentation QM/MM approach. Rsc Adv.,2016, 6, 108590-108602.
18. Fang, Y. F.; Kong, Y. Y.; Xi, J. B.; Zhu, M. L.;Zhu, T.; Jiang, T. T.; Frett, B., Hu, W.; Li, H. Y.*, Ma, M. L.*; Zhang, X. W.*, Preclinical activity of MBM-5 in gastrointestinal cancer by inhibiting NEK2 kinase activity. Oncotarget,2016, 7, 79313-79327.


2015
17.Zhu, T.; Zhang, J. Z. H.; He, X.*, Quantum Calculation of Protein NMR Chemical Shifts Based on the Automated Fragmentation Method. In Advance in Structural Bioinformatics,Wei, D.; Xu, Q.; Zhao, T.; Dai, H., Eds. 2015; Vol. 827, pp 49-70.
16. Swails, J.;Zhu, T.;He, X.*; Case, D. A.*, AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules. J.Biomol. NMR,2015, 63, 125-139.
15. Liu, J.;Zhu, T*.; Wang, X.; He, X.*; Zhang, J. Z. H*., Quantum Fragment Based ab Initio Molecular Dynamics for Proteins. J. Chem. Theory Comput.,2015, 11, 5897-5905.
14. Chen, J. Z.*; Wang, X.;Zhu, T.*;Zhang, Q. G.; Zhang, J. Z. H., A Comparative Insight into Amprenavir Resistance of Mutations V32I, G48V, I50V, I54V, and I84V in HIV-1 Protease Based on Thermodynamic Integration and MM-PBSA Methods. J. Chem. Inf. Model.,2015, 55, 1903-1913.


2010-2014
13.Zhu, T.;Zhang, J. Z. H.; He, X.*, Correction of erroneously packed protein's side chains in the NMR structure based on ab initio chemical shift calculations.Phys.Chem. Chem. Phys.,2014, 16, 18163-18169.
12. He, X.*;Zhu, T.;Wang, X.; Liu, J.; Zhang, J. Z. H.*, Fragment Quantum Mechanical Calculation of Proteins and Its Applications. Accounts Chem. Res.,2014, 47, 2748-2757.
11. Duan, L. L.;Zhu, T.; Zhang, Q. G.; Tang, B.*; Zhang, J. Z. H.*, Electronic polarization stabilizes tertiary structure prediction of HP-36. J. Mol. Model.,2014, 20.
10. Chen, J.; Chen, H.;Zhu, T.;Zhou, D.; Zhang, F.; Lao, X.*; Zheng, H.*, Asp120Asn mutation impairs the catalytic activity of NDM-1 metallo-beta-lactamase: experimental and computational study. Phys. Chem. Chem. Phys.,2014, 16, 6709-6716.
9.Zhu, T.; Zhang, J. Z. H.; He, X.*, Automated Fragmentation QM/MM Calculation of Amide Proton Chemical Shifts in Proteins with Explicit Solvent Model. J. Chem. Theory Comput.,2013, 9, 2104-2114.
8.Zhu, T.;Xiao, X.; Ji, C. G.*; Zhang, J. Z. H.*, A New Quantum Calibrated Force Field for Zinc-Protein Complex.J. Chem. Theory Comput.,2013, 9, 1788-1798.
7. Duan, L. L.;Zhu, T.; Mei, Y.*; Zhang, Q. G.; Tang, B.; Zhang, J. Z. H.*, An implementation of hydrophobic force in implicit solvent molecular dynamics simulation for packed proteins. J. Mol. Model.,2013, 19, 2605-2612.
6.Zhu, T.;He, X.*; Zhang, J. Z. H.*, Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation. Phys. Chem. Chem. Phys.,2012, 14, 7837-7845.
5.Zhu, T.; Hu, G. D.; Zhang, Q. G.*, Quasi-classical Trajectory Study of Reaction O (P-3) plus HCl (v=2; j=1, 6, 9) -> OH plus Cl. Chinese Phys. Lett.,2010, 27.
4. Zhu, T.;Hu, G. D.; Chen, J. Z.; Liu, X. G.; Zhang, Q. G.*, Theoretical study of stereodynamics for reaction O(P-3)+HCl. Chinese Phys. B,2010, 19.
3.Zhu, T.;Hu, G.; Zhang, Q. G.*, Quasi-classical trajectory study of the reaction O(P-3) plus HCl -> OH + Cl and O(P-3) plus DCl -> OD plus Cl: Vector and scalar properties. J. Mol. Struc-Theochem,2010, 948, 36-42.
2. Liu, H.; Liu, X.; Zhu, T.;Sun, H.; Zhang, Q. G.*, THE EFFECT OF VIBRATIONAL EXCITATION OF THE REACTION O(P-3)+HCl -> OH plus Cl FOR THE (3)A '' ELECTRONIC STATES.J. Theor. Comput. Chem.,2010, 9, 1033-1042.
1. Hu, G.-D.;Zhu, T.; Zhang, S. L.; Wang, D.; Zhang, Q. G.*, Some insights into mechanism for binding and drug resistance of wild type and I50V V82A and I84V mutations in HIV-1 protease with GRL-98065 inhibitor from molecular dynamic simulations. Eur. J. Med. Chem.,2010, 45, 227-235.

专利
WO2016/173562PI4KIII-alpha 蛋白及相关膜蛋白复合体在治疗阿尔兹海默病中的应用


软件著作权
软著登字第**号基于反应分子动力学模拟轨迹的反应网络自动构建和可视化软件 ReacNetGenerator


荣誉及奖励
2019第25届上海市大学生化学化工优秀论文交流会一等奖 (曾晋哲)
2019第11届上海市大学生计算机应用能力大赛一等奖 (曾晋哲&肖进)
2019第12届中国大学生计算机设计大赛一等奖 (曾晋哲&肖进)



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