X. Luo, X. Wang, Y. Yao, X. Gao, L. Zhang*, “Unveiling the Template-Dependent Inhibition on the Viral Transcription of SARS-CoV2”, J. Phys. Chem. Lett., 13 (31), 7197-7205 (2022)

X. Luo, T. Xu, X. Gao, L. Zhang*, “Alternative Role of Motif B in Template Dependent Polymerase Inhibition”, Chin. J. Chem. Phys., 35 (3), 407-412 (2022)

Y. Li, D. Zhang, X. Gao, X. Wang, L. Zhang*, “2’- and 3’-Ribose Modifications of Nucleotide Analogues Establish the Structural Basis to Inhibit the Viral Replication of SARS-CoV-2”, J. Phys. Chem. Lett., 13 (18), 4111-4118 (2022) 

Y. Wang, C. Yuan, X. Xu, T. H. Chong, L. Zhang, P. P.-H. Cheung*, X. Huang*, “The Mechanism of Action of T-705 as a Unique Delayed Chain Terminator on Influenza Viral Polymerase Transcription”, Biophys. Chem., 227, 106652 (2021)

L. Zhang*, D. Zhang, X. Wang, C. Yuan, Y. Li, X. Jia, X. Gao, H.-L. Yen, P. P.-H. Cheung*, X. Huang*, “1’-Ribose Cyano Substitution Allows Remdesivir to Effectively Inhibit Nucleotide Addition and Proofreading during SARS-CoV-2 Viral RNA Replication.”, Phys. Chem. Chem. Phys., 23 (10), 5852-5863 (2021)

L. Wang^#, J. Zhang^#, M.-J. Han^#, L. Zhang^#, C. Chen^#, A. Huang^#, R. Xie, G. Wang, J. Zhu, Y. Wang, X. Liu*, W. Zhuang*, Y. Li*, J. Wang*, “A Genetically Encoded Two Dimensional Infrared Probe for Enzyme Active-Site Dynamics”, Angew. Chem. Int. Ed., 60 (20), 11143-11147 (2021)

S. Peng^#, X. Wang^#, L. Zhang*^#, S. Wu, X. Zhao*, X. Huang*, C. Chen*, “Target Search and Recognition Mechanisms of Glycosylase AlkD Revealed by Scanning FRET-FCS and Markov State Models”, Proc. Nat. Acad. Sci. U.S.A. 117 (36), 21889–21895 (2020)

L. Zhang*^#, S. Wu^#, Y. Feng^#, D. Wang, X. Jia, Z. Liu, J. Liu, W. Wang*, “Ligand-bound Glutamine Binding Protein Assumes Multiple Metastable Binding Sites with Different Binding Affinities”, Commun. Biol., 3, 419 (2020)

X. Zhang, Z. Wang, Z.-N. Chen, H. Li, L. Zhang, J. Ye, Q. Zhang*, W. Zhuang*, “Molecular Mechanism of Water Reorientation Dynamics in Dimethyl Sulfoxide Aqueous Mixtures”, J. Phys. Chem. B, 124 (9), 1806–1816 (2020)

F. Long, Z. Chen, K. Han *, L. Zhang *, W. Zhuang*, “Differentiation between Enamines and Tautomerizable Imines Oxidation Reaction Mechanism using Electron-Vibration-Vibration Two Dimensional Infrared Spectroscopy”, Molecules, 24 (5), 869 (2019)

S.-T. Hsieh, L. Zhang, D.-W. Ye, X. Huang*, Y.-C. Cheng*, “A Theoretical Study on the Dynamics of Light Harvesting in the Dimeric Photosystem II Core Complex: Regulation and Robustness of Energy Transfer Pathways”, Faraday Discuss., 216, 94–115 (2019)

X. Chen, J. Song, Z.-N. Chen, T. Jin, F. Long, H. Xie, Y. Zheng*, W. Zhuang*, L. Zhang*, “Rational Designing of 8-Hydroxyquinolin-Imidazolinone-Based Fluorescent Protein Mutants with Dramatically Red: A Computational Study”, J. Comput. Chem., 39, 2307–2315 (2018)

X. Zhang, L. Zhang, T. Jin, Q. Zhang* & W. Zhuang*, “Cosolvent Effect on the Dynamics of Water in Aqueous Binary Mixtures”, Mol. Phys., 116 (7-8), 1014–1025 (2018)

Q. Zhang^#, Z. Pan^#, L. Zhang^#, R. Zhang, Z.-N. Chen, T. Jin, T. Wu, X. Chen, W. Zhuang, “Ion Effect on the Dynamics of Water Hydrogen Bonding Network: A Theoretical and Computational Spectroscopy Point of View”, WIREs Comput. Mol. Sci., e1373 (2018)

V. Molodtsov, E. Sineva, L. Zhang, X. Huang, M. Cashel, S. E. Ades, Murakami, K. S., “Allosteric Effector ppGpp Potentiates the Inhibition of Transcript Initiation by DksA”, Mol. Cell, 69 (5), 828 (2018)

X. Zhang^#, L. Zhang^#, T. Jin, Z. Pan, Z.-N. Chen, Q. Zhang*, and W. Zhuang*, “Salting-in/Salting-out Mechanism of Carbon Dioxide in Aqueous Electrolyte Solutions”, Chinese J. Chem. Phys., 30, 811 (2017)

A. Chevalier, D.-A. Silva, G. J. Rocklin, D. R. Hicks, R. Vergara, P. Murapa, S. M. Bernard, L. Zhang, K. H. Lam, G. Yao, C.D. Bahl, S.I. Miyashita, I. Goreshnik, J.T. Fuller, M.T. Koday, C. M. Jenkins, T. Colvin, L. Carter, A. Bohn, C.M. Bryan, D. A. Fernández-Velasco, L. Stewart, M. Dong, X. Huang, R. Jin, I. A. Wilson, D. H. Fuller, D. Baker, “Massively parallel de novo protein design for targeted therapeutics”, Nature, 550, 74–79, (2017)

X. Zheng, L. Zhu, X. Zeng, L. Meng, L. Zhang, D. Wang, X. Huang, “Kinetics-Controlled Amphiphile Self-Assembly Processes”, J. Phys. Chem. Lett., 8, 1798–1803 (2017)

Y. Feng^#, L. Zhang^#, S. Wu, Z. Liu, X. Gao, X. Zhang, M. Liu, J. Liu, X. Huang*, W. Wang*, “Conformational Dynamics of apo-GlnBP Revealed by Experimental and Computational Analysis”, Angew. Chem. Int. Ed. 55 (45), 13990–13994 (2016)

H. Lin, S. Chen, H. Hu, L. Zhang, T. Ma, J. Y. L. Lai, Z. Li, A. Qin, X. Huang, B. Tang, and H. Yan, “Reduced Intramolecular Twisting Improves the Performance of 3D Molecular Acceptors in Non-Fullerene Organic Solar Cells”, Adv. Mater. 28 (38), 8546-8551 (2016)

L. Zhang, H. Jiang, F. K. Sheong, F. Pardo-Avila, P. P.-H. Cheung, X. Huang, “Constructing Kinetic Network Models to Elucidate Mechanisms of Functional Conformational Changes of Enzymes and their Recognition with Ligands”, Book Chapter, Methods Enzymol., Computational approaches for studying Enzyme Mechanism, (Editor G.A. Voth), 578, 343–371 (2016)  

L. Zhang, F. Pardo-Avila, C. I. Unarta, P.-H. P. Cheung, G. Wang, D. Wang, and X. Huang, “Elucidation of the Dynamics of Transcription Elongation by RNA Polymerase II using Kinetic Network Models”, Acc. Chem. Res. 49 (4), 687–694 (2016)

L.-T. Da, F. Pardo-Avila, L. Xu, D.-A. Silva, L. Zhang, X. Gao, D. Wang, X. Huang, “Bridge Helix Bending Promotes RNA Polymerase II Backtracking through a Critical and Conserved Threonine Residue”, Nat. Commun. 7, 11244 (2016)

C. Hwang, L. Xu, W. Wang, S. Ulrich, L. Zhang, J. Chong, J. H. Shin, X. Huang, E. Kool, C. McKenna, D. Wang, “Functional Interplay between NTP Leaving Group and Base Pair Recognition during RNA Polymerase II Nucleotide Incorporation Revealed by Methylene Substitution”, Nucl. Acids Res. 44 (8), 3820-3828 (2016)

L. Zhang, D.-A. Silva, F. Pardo-Avila, D. Wang, X. Huang, “Structural Model of RNA Polymerase II Elongation Complex with Complete Transcription Bubble Reveals NTP Entry Routes”, PLoS. Comp. Bio. 11, e1004354 (2015)

J. Zhao, Y. Li, J. Zhang, L. Zhang, J.Y.L. Lai, K. Jiang, C. Mu, Z. Li, C.L.C. Chan, A. Hunt, S. Mukherjee, H. Ade, X. Huang, H. Yan, “The Influence of Spacer Units on Molecular Properties and Solar Cell Performance of non-Fullerene Acceptors”, J. Mater. Chem. A 3, 20108-20112 (2015)

L. Xu, W. Wang, L. Zhang, J. Chong, X. Huang, D. Wang, “Impact of Template Backbone Heterogeneity on RNA Polymerase II Transcription”, Nucl. Acids Res. 43 (4), 2232-2241 (2015)

Y. Liu, C. Mu, K. Jiang, J. Zhao, Y. Li, L. Zhang, Z. Li, J. Lai, H. Hu, T. Ma, R. Hu, D. Yu, X. Huang, B. Tang, H. Yan, “A Tetraphenylethylene Core-based 3D Structure Small Molecular Acceptor Enabling Efficient non-Fullerene Organic Solar Cells”, Adv. Mater. 27 (6), 1015-1020 (2015)

L. Zhang, D.-A. Silva, A. Yue, H. Zhang, Y.J. Yan, X. Huang, “Dynamic Protein Conformations Preferentially Drive Energy Transfer along Active Chain of the Photosystem-II Reaction Center”, Nat. Commun. 5, 4170 (2014)

L. Xu, L. Zhang, J. Chong, J. Xu, X. Huang, D. Wang, “Strand-specific (asymmetric) contribution of phosphodiester linkages on RNA polymerase II transcriptional efficiency and fidelity”, Proc. Nat. Acad. Sci. U.S.A. 111, E3269–E3276 (2014)

L. Zhang, D.-A. Silva, Y.J. Yan, X. Huang, “Force Field Development for Cofactors in the Photosystem II”, J. Comput. Chem. 33 (25), 1969–1980 (2012)