Publications

(*Corresponding authors, #Authors with equal contributions)

61. Unveiling intracellular phase separation: advances in optical imaging of biomolecular condensates”, submitted.

60. Synchronous assembly of peptide anisosome”, submitted.

59. The mTORC1 coordinates de novo purine biosynthesis with lysosome mediated purine recycling to resist chemotherapy”, submitted.

58. Microenvironment-governed photo-uncaging reaction for suborganelle protein proximity labeling”, in review.

57. “Tailoring the pKa of fluorescence lifetime imaging probes to visualize aggrephagy and resolve its microenvironmental viscosity”, in revision.


56. “Time-resolved fluorescent proteins towards fluorescence microscopy in the temporal and spectral domains”, in revision.


55. Live-cell visualization of tau aggregation in human neurons”, in revision.


54. L. Zhu, Y. Pan, Z. Hua, Y. Liu, X. Zhang*, Ionic effect on the microenvironment of biomolecular condensates”, J. Am. Chem. Soc., 2024, in press.

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53. J. Ma#F. Luo#, C. -H. Hsiung, J. Dai, Z. Tan, S. Ye, L. Ding*, B. Shen*, X. Zhang*, “Chemical control of fluorescence lifetime towards multiplexing imaging”, Angew. Chem. Int. Ed., 2024, e202403029.

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52. Y. Huang, M. Chang, X. Gao, J. Fang, W. Ding, J. Liu, B. Shen*, X. Zhang*, NRhFluors: Quantitative revealing the interaction between protein homeostasis and mitochondria dysfunction via fluo-rescence lifetime imaging, ACS Cent. Sci., 2024, 10, 4, 842-851.




51. H. Feng, Q. Zhao, N. Zhao, Z. Liang, Y. Huang, X. Zhang, L. Zhang*, Y. Liu*, “A cell-permeable photosensitizer for selective proximity labeling and crosslinking of aggregated proteome”, Adv. Sci., 2024, 2306950.




50. J. Ma#, R. Sun#, K. Xia#, Q. Xia#, Y. Liu*, X. Zhang*, Design and application of fluorescent probes to detect cellular physical microenvironments”, Chem. Rev., 2024, 124, 4, 1738–1861.



49. Y. Huang, J. Chen, C. -H. Hsiung, Y. Bai, Z. Tan, S. Ye, X. Zhang*, Detecting protein-protein interaction during liquid-liquid phase separation using fluorogenic protein sensors”, Mol. Biol. Cell, 2024, 35, 3, ar41.


48. C. Hoelzel#, Y. Bai#, M. Wang, Y. Liu*, X. Zhang*, High-fidelity assay based on turn-off fluorescence to detect the perturbations of cellular proteostasis”, ACS Bio. & Med. Chem. Au., 2024, 4, 2, 111-118.




47. J. Wang, X. Ma, Y. Hu, G. Feng, C. Guo, X. Zhang, H. Ma*, Regulation of micro- and small-exon retention and other splicing processes by GRP20 for flower development”, Nat. Plants, 2024, 10, 66-85.


46. X. Zhang*, S. Booker*, Seeing is believing: advances in biological imaging”, ACS Bio. & Med. Chem. Au, 2024, 4, 1-3.


45. X. Cheng, Y. Pu, S. Ye, X. Xiao, X. Zhang, H. Chen*, “Measuring solvent exchange in silica nanoparticles with rotor-based fluorophore”, Adv. Mater., 2023, 2305779.

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44. A. P. Latham, L. Zhu, D. A. Sharon, S. Ye, A. P. Willard, X. Zhang*, B. Zhang*, “Frustrated microphase separation produces interfacial environment within biological condensates”, eLife, in press.


43. J. Dai, X. Zhang*, “Chemical regulation of fluorescence lifetime”, ACS Chemical & Biomedical Imaging, 2023, 1, 9, 796–816.



42. Y. Bai#, S. Zhang#, H. Dong#, Y. Liu, C. Liu*, X. Zhang*, “Advanced techniques for detecting protein misfolding and aggregation in cellular environments”, Chem. Rev., 2023, 123, 21, 12254-12311.


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41. S. Ye, A. P. Latham, Y. Tang, C.-H. Hsiung, J. Chen, F. Luo, Y. Liu, B. Zhang, X. Zhang*, Micropolarity governs the structural organization of biomolecular condensates”, Nat. Chem. Biol., 2024, 20, 443-451.




40. X. Zhang* and B. Tang* et al., “Aggregation-Induced Emission (AIE), Life and Health”, ACS Nano, 2023, 17, 15, 14347–14405.




39. C. Liu*, X. Zhang*, “Navigating the terrain of protein aggregation and phase separation - A chemical biology perspective”, Curr. Protoc. Chem. Biol., 2023, 77, 102386.


38. Q. Ma, M. Wang, Y. Huang, Y. Nie, X. Zhang, D. D. Yang, Z. Wang, S. Ding, N. Qian, Y. Liu*, X. Pan*, “Identification of a novel transthyretin mutation D39Y in a cardiac amyloidosis patient and its biochemical characterizations”, Front. Cardiovasc. Med., 2023, 10, 1091183.


37. K. H. Jung, J. Sun, C. -H. Hsiung, X. L. Lian, Y. Liu, X. Zhang*, “Nuclear bodies protect phase separated proteins from degradation in stressed proteome”, eLife, 2023, in press.


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36. B. Shen, L. Liu, Y. Huang, J. Wu, H. Feng, Y. Liu*, H. Huang*, X. Zhang*, “Installing hydrogen bonds as a general strategyto control viscosity sensitivity of molecular rotor fluorophores”, Aggregate, 2024, e421.


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35. D. Shen, Q. Zhao, M. Wang, B. Zhong, W. Jin, Y. Huang, H. Jin, B. Jing, W. Wan, X. Zhang, L. Zhang*, Y. Liu*, Developing an affinity-based chemical proteomics method to in-situ capture amorphous aggregated proteome and profile its heterogeneity in stressed cells”, Anal. Chem., 2023, 95, 15, 6358–6366.


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34. Z. Zhang, L. Zhu, J. Feng, H. Zhang, X. Zhang, J. Sun, B. Tang*, “In situ monitoring of protein aggregation via clusteroluminescence”, Mat. Chem. Front., 2023, 7, 713-719.


33. Y. Bai, W. Wan, Y. Huang, J. Wu, L. Liu, B. Jing, J. Chen, X. Zhang*, Y. Liu*, “Tailoring the positive and negative solvatochromism for chalcone analogues to detect heterozygous protein co-aggregation”, ChemComm, 2023, 59, 4016 – 4019.



32. H. Feng, Q. Zhao, B. Zhang, H. Hu, M. Liu, K. Wu, X. Li, X. Zhang*, L. Zhang*, Y. Liu*, “Enabling photo-crosslinking and photo-sensitizing properties for synthetic fluorescent protein chromophores”, Angew. Chem. Int. Ed., 2023, 62, 2, e202215215.


31. B. Shen, K. H. Jung, S. Ye, C. A. Hoelzel, C. H. Wolstenholme, H. Huang*, Y. Liu*, X. Zhang*, “A dual-functional BODIPY-based molecular rotor probe reveals different viscosity of protein aggregates in live cells”, Aggregate, 2023, e301.



30. L. Liu, Y. Huang, Y. Zhou, Y. Zhao, J. Qia, X. Zhang*, B. Shen*, “Fluorogenic toolbox for visualizing protein aggregation: From designing principles to biological application”, Trends in Anal. Chem., 2022, 157, 116764.

29. L. Wang, C.-H. Hsiung, X. Liu, S. Wang, A. Loredo, X. Zhang*, H. Xiao*, “Xanthone-based solvatochromic fluorophores for quantifying micropolarity of protein aggregates”, Chem. Sci., 2022, 13, 12540.



28. E. Pinho Melo*, T. Konno, I. Farace, M. Ali Awadelkareem, L. R. Skov, F. Teodoro, T. P. Sancho, A. W. Paton, J. C. Paton, M. Fares, P. M. R. Paulo, X. Zhang, E. Avezov*,Stress-induced protein disaggregation in the Endoplasmic Reticulum catalysed by BiP”, Nat. Comm., 2022, 13, 2501.


27. S. Ye, Y. Tang, X. Zhang*, “Principles, modulation and applications of fluorescent protein chromophores”, Chem Phys Rev, 2022, 3, 011308.


26. S. Ye, C. -H. Hsiung, Y. Tang, X. Zhang*, “Visualize the multi-step process of protein aggregation in live cells”, Acc. Chem. Res., 2022, 55, 381–390.



25. W. Dion, H. Ballance, J. Lee, Y. Pan, S. Irfan, C. Edwards, M. Sun, J. Zhang, X. Zhang, S. Liu, B. Zhu*, Four-dimensional nuclear speckle phase separation dynamics regulate proteostasis", Sci. Adv., 2022, 8, eabl4150.




24. Y. Jiang, C. Chen, L. N. Randolph, S. Ye, X. Zhang, X. Bao*, X. Lian*, “Generation of pancreatic progenitors from human pluripotent stem cells by small molecules”, Stem Cell Rep., 2021, 16, 2395-2409.




23. S. Tang*, W. Wang, X. Zhang*, “Direct visualization and profiling of protein misfolding and aggregation in live cells”, Curr. Opin. Chem. Biol., 2021, 64, 116-123.


22. G. C. Carter, C. Hsiung, L. W. Simpson, H. Yang, X. Zhang*, “N-terminal domain of TDP43 enhances liquid-liquid phase separation of globular proteins, J. Mol. Biol., 2021, 433, 166948.        



21. S. Tang, S. Ye, X. Zhang*, “When aggregation-induced emission meets protein aggregates”, Nat. Sci. Rev., 2021, 8, 6, nwab013.

20. S. Ye, H. Zhang, J. Fei, C. Wolstenholme, X. Zhang*, “A general strategy to control viscosity sensitivity of molecular rotor-based fluorophores”, Angew. Chem. Int. Ed., 2021, 60, 1339-1346.                



19. C. H. Wolstenholme, H. Hu, S. Ye, B. E. Funk, D. Jain, C. -H. Hsiung, G. Ning, Y. Liu*, X. Li*, X. Zhang*, “AggFluor: Fluorogenic toolbox enables direct visualization of the multi-step protein aggregation process in live cells”, J. Am. Chem. Soc., 2020, 142, 17515–17523.(highlighted by JACS Spotlights, Protein Aggregation: It’s a Process)                  


18. C. A. Hoelzel, X. Zhang*, “Visualizing and manipulating biological processes using HaloTag and SNAP-Tag technologies, ChemBioChem, 2020, 21, 1935-1946.                            



17. K. H. Jung, X. Zhang*, “Fluorogenic detection of protein aggregates in live cells using the AggTag method, Methods Enzymol., 2020, 639, 1-22.                            



16. C. A. Hoelzel, H. Hu, C. H. Wolstenholme, B. A. Karim, K. T. Munson, K. H. Jung, H. Zhang, Y. Liu, H. P. Yennawar, J. B. Asbury, X. Li*, X. Zhang*,“A general strategy to enhance donor-acceptor molecules using solvent-excluding substituents, Angew. Chem. Int. Ed., 2020, 59, 4785-4792.                            


15. S. H. Kim, Y. Liu, C. Hoelzel, X. Zhang*, T. -H. Lee*, “Super-resolution optical lithography with DNA, ACS Nano Letter, 2019, 19, 6035-6042.                           



14. K. H. Jung, S. F. Kim, Y. Liu, X. Zhang*, “A fluorogenic AggTag method based on Halo- and SNAP-tag to simultaneously detect the aggregation of two proteins in live cells, ChemBioChem, 2019, 20, 1078-1087. 



13. K. H. Jung, M. Fares, L. S. Grainger, C. H. Wolstenholme, A. Hou, Y. Liu, X. Zhang*, “A SNAP-tag fluorogenic probe mimicking the chromophore of the red fluorescent protein Kaede, Org. Biomol. Chem., 2019, 17, 1906-1915. 



12. Y. Liu, M. Fares, X. Zhang*, “Monitoring proteome stress in live cells using HaloTag-based fluorogenic sensor”, Methods Mol. Biol., 2019, 1873, 171-182.                             



11. M. Fares, X. Zhang*, “Quantification of cellular proteostasis in live cells by fluorogenic assay using the AgHalo sensor, Curr. Protoc. Chem. Biol., 2019, 11, e58.

10. H. Hu, C. H. Wolstenholme, X. Zhang*, X. S. Li*, “Inverted solvatochromic stokes shift in GFP-like chromophores with extended conjugation, Chin. J. Chem. Phys., 2018, 31, 599-607.                            



9. Y. Liu, K. Miao, Y. Li, M. Fares, S. Chen, X. Zhang* “A HaloTag-based multi-color fluorogenic sensor visualizes and quantifies proteome stress in live cells using solvatochromic and molecular rotor-based fluorophores, Biochemistry, 2018, 57, 4663-4674. 



8. B. I. Leach, X. Zhang, J. W. Kelly, H. J. Dyson, P. E. Wright*, “NMR measurements reveal the structural basis of transthyretin destabilization by pathogenic mutations, Biochemistry, 2018, 57, 4421-4430.



7. Y. Liu, C. H. Wolstenholme, G. Carter, H. Liu, H. Hu, L. S. Grainger, K. Miao, M. Fares, C. A. Hoelzel, H. Yennawar, G. Ning, M. Du, L. Bai, X. Li, X. Zhang*, “Modulation of fluorescent protein chromophores to detect protein aggregation with turn-on fluorescence, J. Am. Chem. Soc., 2018, 140, 7381-7384.                                                           



6. A. Pedley, G. Karras, X. Zhang, S. Lindquist, S. Benkovic*, “Role of HSP90 in the regulation of de novo purine biosynthesisBiochemistry, 2018, 57, 3217-3221.



5. X. Li, T. Wang, P. Duan, M. Baldini, H. Huang, B. Chen, S. Juhl, D. Koeplinger, V. Crespi, K. Schmidt-Rohr, R. Hoffmann, N. Alem, M. Guthrie, X. Zhang, J. Badding*, “Carbon nitride nanothread crystals derived from pyridine”, J. Am. Chem. Soc., 2018, 140, 4969-4972.                                                                                                               


4. Y. Liu, X. Zhang*, “Heat shock protein reports on proteome stress”, Biotechnology J, 2018, 13, 1800039.                            



3. M. Fares, Y. Li, Y. Liu, K. Miao, Z. Gao, Y. Zhai, X. Zhang*, “A molecular rotor-based Halo-tag ligand enables a fluorogenic proteome stress sensor to detect protein misfolding in mildly stressed proteome, Bioconjutate Chem., 2018, 29, 215-224.             



2. Y. Liu, M. Fares, N. P. Dunham, Z. Gao, K. Miao, X. Jiang, S. S. Bollinger, A. K. Boal, X. Zhang*, “AgHalo: A facile fluorogenic sensor to detect drug induced proteome stress, Angew. Chem. Int. Ed., 2017, 56, 8672-8676.                                                         



1. Y. Liu, K. Miao, N. P. Dunham, H. Liu, M. Fares, A. B. Boal, X. Li, X. Zhang*,  “The cation-π interaction enables a Halo-Tag fluorogenic probe for fast no-wash live cell imaging and gel-free protein quantification, Biochemistry, 2017, 56, 1585-1595, (ACS Editor’s Choice). Featured by Viewpoint in Biochemistry.                            





From Scripps and Caltech:


36. Y. Liu#, X. Zhang#, W. T. Chen, Y. L. Tan, J. W. Kelly*, “Fluorescence turn-on folding sensor to monitor proteome stress in live cells”, J. Am. Chem. Soc., 2015, 137, 35, 11303-11311. 




35. Y. H. Cho, X. Zhang, Y. Liu, K. Fayer, D. L. Powers, J. W. Kelly, L. Gierasch*., E. T. Powers*, “Individual and collective contributions of chaperonin and degradation to protein homeostasis in E. coli, Cell Reports, 2015, 11, 2, 321-333.

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34. Y. Liu#, Y. L. Tan#, X. Zhang#, G. Bhabha, D. Ekiert, J. C. Genereux, Y. H. Cho, Y. Kipnis, S. Bjelic, D. Baker, J. W. Kelly*, “Small molecule probes to quantify the functional fraction of a specific protein in a cell with minimal folding equilibrium shifts”, Proc. Natl. Acad. Sci. (USA), 2014, 111, 12, 4449-4454.

33. X. Zhang, Y. Liu, J. C. Genereux, C. Nolan, M. Singh, J. W. Kelly*, “Heat-shock response transcriptional program enables high-yield and high-quality recombinant protein production in Escherichia coli”, ACS Chem. Biol., 2014, 9, 1945−1949. (ACS Editor’s Choice)


32. Y. Liu#, X. Zhang#, Y. L. Tan, G. Bhabha, D. Ekiert, Y. Kipnis, S. Bjelic, D. Baker, J. W. Kelly*, “De novo designed enzymes as small molecule-regulated fluorescence imaging tags and fluorescent reporters”, J. Am. Chem. Soc., 2014, 136, 38, 13102-13105. (co-first authors).


31. X. Zhang, J. W. Kelly*, “Chaperonins resculpt folding free energy landscapes to avoid kinetic traps and accelerate protein foldingJ. Mol. Biol., 2014, 426, 15, 2736-2738.


30. X. Zhang, S. Shan*, “Fidelity of co-translational protein targeting by the signal recognition particle”, Ann. Rev. Biophysics, 2014, 43, 381-408.

29. D. Akopian#, K. Shen#, X. Zhang#, S. Shan*, “Signal recognition particle: An essential targeting machine”, Ann. Rev. Biochemistry, 2013, 82, 693-721. (#co-first authors listed alphabetically)


28. X. Li*, X. Zhang, A. R. Ladiwala, D. Du, J. Yadav, P. Tessier, P. Wright, J. W. Kelly, J. Buxbaum*, “Mechanism of transthyretin inhibition of β-amyloid aggregation in vitro”, J. Neuroscience, 2013, 33, 50, 19423-19433.

27. O. von Loeffelholz, K. Knoops, A. Ariosa, X. Zhang, M. Karuppasamy, K. Huard, G. Schoehn, I. Berger, S. Shan*, C. Schaffitzel*, “Structural basis of signal sequence surveillance and selection by the SRP-FtsY complex”, Nat. Struct. Mol. Biol.2013, 20, 604-610.

26. X. Liu#, W. Wei#, Q. Yuan, X. Zhang, N. Li, Y. Du, G. Ma, C. Yan, D. Ma*, “Apoferritin–CeO2 nano-truffle that has excellent artificial redox enzyme activity”, Chem. Comm., 2012, 48, 3155-3157.

25. X. Zhang, V. Q. Lam, Y. Mou, T. Kimura, J. Chung, S. Chandrasekar, J. R. Winkler, S.L. Mayo, S. Shan*, “Direct visualization reveals dynamics of a transient intermediate during protein assembly”, Proc. Natl. Acad. Sci. (USA), 2011, 108, 16, 6450-6455.

24. K. Shen, X. Zhang, S. Shan, “Synergistic actions between the SRP RNA and translating ribosome allow efficient delivery of the correct cargos during co-translational protein targeting”, RNA, 2011, 17, 5, 892-902.

23. M. J. Yang, X. Zhang*, “Molecular dynamics simulations reveal structural coordination of Ffh-FtsY heterodimer towards GTPase activation”, Proteins: Struc., Funct., Bioinf., 2011, 79, 6, 1774-1785. 

22. M. J. Yang, X. Q. Pang, X. Zhang, K. Han*, “Molecular dynamics simulation reveals preorganization of the Chloroplast FtsY towards complex formation induced by GTP-binding”, J. Struct. Biol., 2011, 173, 1, 57-66.

21. X. Zhang, R. Rashid, K. Wang, S. Shan*, “Sequential checkpoints govern substrate selection during co-translational protein targeting”, Science, 2010, 328, 5979, 757-760.

20. M. J. Yang, X. Zhang, K. Han*, “Molecular dynamics simulation of SRP GTPases: towards an understanding of complex formation from equilibrium fluctuations”, Proteins: Struc., Funct., Bioinf., 2010, 78, 10, 2222-2237.

19. X. Zhang, C. Schaffitzel, N. Ban, S. Shan*, “Multiple conformational switches in a GTPase complex control co-translational protein targeting”, Proc. Natl. Acad. Sci. (USA)2009, 106, 6, 1754-1759.

18. S. Shan*, S. L. Schmid, X. Zhang, “Signal recognition particle (SRP) and SRP receptor: A new paradigm for multi-state regulatory GTPases”, Biochemistry, 2009, 48, 29, 6696–6704.

17. E. L. Wu, K. Wong, X. Zhang, K. Han*, J. Gao*, “Determination of the structure form of the fourth ligand of zinc in acutolysin a using combined quantum mechanical and molecular mechanical simulation”, J. Phys. Chem. B2009, 113, 8, 2477–2485.

16. X. Zhang, S. Kung, S. Shan*, “Demonstration of a multistep mechanism for assembly of the SRP•SRP receptor complex: Implications for the catalytic role of SRP RNA”, J. Mol. Biol., 2008, 381, 3, 581-593.

15. X. Zhang, K. Han*, “High-order symplectic integration in quasi-classical trajectory simulation: Case study for O(1D)+H2, Int. J. Quant. Chem., 2006, 106, 8, 1815-1819.

14. T. Chu, X. Zhang, L. Ju, L. Yao, K. Han*, M. Wang, J. Z. H. Zhang*, “First principles quantum dynamics study reveals subtle resonance in polyatomic reaction: The case of F+CH4 → HF+CH3”, Chem. Phys. Lett., 2006, 424, 4-6, 243-246.


13. X. Chen, X. Zhang, K. Han*, A. J. C. Varandas*, “ab initio study of the H+ClONO2 reaction, Chem. Phys. Lett., 2006, 421, 4-6, 453-59.

12. L. Ju, T. Xie, X. Zhang, K. Han*, “A modified potential energy surface for the C2H+H2↔ C2H2+H reaction and a theoretical study on its rate constants, Chem. Phys. Lett., 2005, 409, 4-6, 249-254.

11. T. Chu, X. Zhang, K. Han*, “A quantum wave-packet study of intersystem crossing effects in the O(3P, 1D)+H2 reaction, J. Chem. Phys., 2005, 122, 21, 214301-214306.

10. G. Yang, L. Yao, X. Zhang, Q. Meng, K. Han*, “Theoretical study of the mechanism for spin-forbidden quenching process O(1D)+CO2 (1Sg+) → O(3P)+CO2 (1Sg+)”, Int. J. Quant. Chem., 2005, 105, 2, 154-159.

9. C. Yang*, X. Zhang, K. Han, “Theoretical study on analytical potential function and spectroscopic parameters for CaF molecule, J. Mol. Struct-Theochem, 2004, 678, 1-3, 183-188.

8. C. Yang*, X. Zhang, K. Han, “ab initio geometries, electronic structures of MgB2 molecule, J. Mol. Struct-Theochem, 2004, 677, 1-3, 11-14.

7. C. Yang*, X. Zhang, K. Han, “Analytical potential energy function and spectroscopic parameters for the ground and excited states of NaH”, J. Mol. Struct-Theochem, 2004, 676, 1-3, 209-213.

6. G. Yang*, X. Zhang, Q. Meng, K. Han, “Theoretical studies on the intermediate complex mechanism of the energy transfer reaction of O(1D)+CO2 (1Sg+) → O(3P)+CO2 (1Sg+)”, Chem. J. Chin. Univ., 2004, 25, 4, 689-692.

5. G. Yang, Q. Meng, X. Zhang, K. Han*, “Theoretical study on the formation mechanism of Iso-CH2l-Cl”, Int. J. Quant. Chem., 2004, 97, 2, 719-724.

4. X. Zhang, G. Yang, K. Han*, M. Wang, J. Z. H. Zhang, “Quantum dynamics study of isotope effect for H + CH4 reaction using the SVRT model, J. Chem. Phys., 2003, 118, 20, 9266-9271.

3. C. Yang*, Y. Huang, X. Zhang, K. Han, “MRCI potential curve and analytical potential energy function of the ground state of H2”, J. Mol. Struct-Theochem, 2003, 625, 1-3, 289-293.

2. X. Zhang, K. Han*, J. Z. H. Zhang, “SVRT calculation for bond-selective reaction H+HOD → H2+OD, HD+OH, J. Chem. Phys., 2002, 116, 23, 10197-10200.

1. X. Zhang, T. Xie, M. Zhao, K. Han*, “Quasiclassical trajectory simulation of the chemical reaction Ba+HF (n, J) → BaF (n‘, J‘)+H”, Chin. J. Chem. Phys., 2002, 15, 3, 169-174.



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