Publications

Selective Publications

See Google Scholar for the full list of publications.

2025

• Liu, B., Boysen, J.G., Unarta, I.C., Du, X., Li, Y., Huang, X.* “Exploring Transition States of Protein Conformational Changes via Out-of-Distribution Detection in the Hyperspherical Latent Space“, Nature Communications, 16, 349, (2025)

2024

• Qiu, Y., Wiewiora, R.P., Izaguirre, J.A., Xu, H., Sherman, W., Tang, W.*, Huang, X.* “Non-Markovian Dynamic Models Identify Non-Canonical KRAS-VHL Encounter Complex Conformations for Novel PROTAC Design“, JACS Au, 4 (10), 3857–3868, (2024)
• Wang, D.,  Qiu, Y., Beyerle, E.R., Huang, X.*, Tiwary, P.* “Information Bottleneck Approach for Markov Model Construction”, J. Chem. Theory Comput., 20 (12), 5352–5367, (2024)

– Virtual special issue “Markov State Modeling of Conformational Dynamics” 

• Wu, Y.,  Cao, S., Qiu, Y., Huang, X.*, “Tutorial on how to build non-Markovian dynamic models from molecular dynamics simulations for studying protein conformational changes”, J. Chem. Phys, 160, 121501, (2024)

– JCP Cover Article & JCP Featured Article 

• Unarta, I.C.,  Cao, S., Goonetilleke, E.C., Niu, J., Gellman, S.H., Huang, X.*, “Submillisecond Atomistic Molecular Dynamics Simulations Reveal Hydrogen Bond-Driven Diffusion of a Guest Peptide in Protein−RNA Condensate”, J. Phys. Chem. B, 128 (10), 2347–2359 (2024)

– Virtual special issue “Gregory A. Voth Festschrift”.

2023

• Cao, S., Qiu, Y., Kalin, M.L., Huang, X.*, “Integrative Generalized Master Equation: A Method to Study Long-timescale Biomolecular Dynamics via the Integrals of Memory Kernels”, J. Chem. Phys.,159, 134106, (2023)

– JCP Featured Article

• Cribari, M.A., Unger, M.J., Unarta, I.C., Ogorek, A.N., Huang, X,. Martell J.D.*, “Ultrahigh-Throughput Directed Evolution of Polymer-Degrading Enzymes Using Yeast Display”, J. Am. Chem. Soc., (2023), DOI: 10.1021/jacs.3c08291
• Liu, Z., Kalin, M.L., Liu, B., Cao, S., Huang, X.*, “Kinetic network models to elucidate aggregation dynamics of aggregation-induced emission systems”, Aggregrate, e422, (2023)
• Liu, B., Xue, M., Qiu, Y., Konovalov, K.A., O’Connor, M.S., Huang, X.*, “GraphVAMPnets for uncovering slow collective variables of self-assembly dynamics”, J. Chem. Phys., 159, 094901, (2023)

– Special issue on “Machine Learning Hits Molecular Simulations”

• Kohn, E.M., Konovalov, K., Gomez, C.A., Hoover, G.N., Yik, A.K., Huang, X., Martell, J.D.*, “Terminal Alkyne-Modified DNA Aptamers with Enhanced Protein Binding Affinities”, ACS Chem. Biol., 18, 9, 1976–1984, (2023)

– Cover article

• Qiu, Y., O’Connor, M.S., Xue, M., Liu, B., Huang, X.*, “An Efficient Path Classification Algorithm Based on Variational Auto-Encoder to Identify Metastable Path Channels for Complex Conformational Changes”, J. Chem. Theory Comput., 19(14), 4728-4742, (2023)

– Special issue on “Machine Learning for Molecular Simulation”

• Konovalov, K.A., Wu, C., Qiu, Y., Balakrishnan, V., Parihar, P., O’Connor, M.S., Xing, Y.*, Huang, X.*, “Disease Mutations and Phosphorylation Alter the Allosteric Pathways Involved in Autoinhibition of Protein Phosphatase 2A”, J. Chem. Phys., 158, 215101, (2023)

– Special issue on “New Views of Allostery”

• Dominic III, A.J.; Cao, S.; Montoya-Castillo, A.*; Huang, X.* “Memory unlocks the future of biomolecular dynamics: Transformative tools to uncover physical insights accurately and efficiently”, J. Am. Chem. Soc., 145(18), 9916-9927 (2023)
• Wu, C.G., Balakrishnan, V.K., …, Huang, X,. Strack, S., Xing, Y., “B56δ long-disordered arms form a dynamic PP2A regulation interface coupled with global allostery and Jordan’s syndrome mutations“, Proc. Nat. Acad. Sci. U.S.A.,  121 (1) e2310727120, (2023)

• Dominic III, A.J.; Sayer, T.; Cao, S.; Markland, T.; Huang, X.; Montoya-Castillo, A.* “Building insightful, memory-enriched models to capture long-time biochemical processes from short-time simulations“, Proc. Nat. Acad. Sci. U.S.A., 120 (12) e2221048120, (2023)

• Cao, S.; Kalin, M.L.; Huang, X.*, “EPISOL: A Software Package with Expanded Functions to Perform 3D-RISM Calculations for the Solvation of Chemical and Biological Molecules“, J. Comput. Chem., 44, 1536-1549, (2023)

– Special issue on “Remembering Sihyun Ham and Protein Computational Science”

• Yik, A.K, Qiu, Y., Unarta, I.C., Cao, S., Huang, X.,*, “A Step-by-step Guide on How to Construct quasi-Markov State Models to Study Functional Conformational Changes of Biological Macromolecules“, Chapter 10, “A Practical Guide to Recent Advances in Multi-scale Modeling and Simulation for Biomolecules”, Edited by Wang, Y. and Zhou, R., AIP Publihing (ChemRxiv), (2023)

• Unarta, I. C.; Goonetilleke, E.C.; Wang, D.*; Huang, X.*, “Nucleotide Addition and Cleavage by RNA Polymerase II: Coordination of Two Catalytic Reactions using a Single Active Site”, J. Bio. Chem., 299(2) 102844, (2023)

2022

• Cao, S.; Qiu, Y.; Unarta, I. C.; Goonetilleke, E.C.; Huang, X.*, “The Ion-Dipole Correction of the 3DRISM Solvation Model to Accurately Compute Water Distributions Around Negatively Charged Biomolecules“, J. Phys. Chem. B., 126(43), 8632, (2022)

– Special issue on “Biomolecular Electrostatic Phenomena”

• Liu, B., Qiu, Y., Goonetilleke, E.C., Huang, X.* , “Kinetic Network Models to Study Molecular Self-assembly in the Wake of Machine Learning“, MRS. Bulletin, 47, 958–966, (2022)

– Special issue on “Artificial Intelligence in Computational Materials Science” & Cover article

• Zheng, X., Chan, M.H., Chan, A.K., Ng, M., Sheong F.K., Li, C., Goonetilleke, E.C., Lam, W., Lau, T.C., Huang, X.,* Yam, V.W.W.*, “Elucidation of the key role of Pt···Pt interactions in the directional self-assembly of platinum(II) complexes“, Proc. Nat. Acad. Sci. U.S.A., 119 (12) e2116543119, (2022)

• Gu, H., Wang, W., Cao, S., Unarta, I.C., Yao, Y., Sheong, F.K.*, Huang, X.,*, “RPnet: a reverse-projection-based neural network for coarse-graining metastable conformational states for protein dynamics“, Phys. Chem. Chem. Phys., 24:1462-1474, (2022)

– Selected as 2022 PCCP HOT article

2021

• Unarta, I.S., Cao, S., Kubo, S., Wang, W., Cheung, P.P.H., Gao, X., Takada, S., Huang, X.* “Role of Bacterial RNA Polymerase Gate Opening Dynamics in DNA Loading and Antibiotics Inhibition Elucidated by quasi-Markov State Model”, Proc. Nat. Acad. Sci. U.S.A., 118(17), e2024324118, (2021)
• Li, C., Liu, Z., Goonetilleke, E.C., Huang, X.* “Temperature-dependent Kinetic Pathways of Heterogeneous Ice Nucleation Competing between Classical and Non-classical Nucleation”, Nature Communications, 12, 4954, (2021)
• Konovalov, K.A., Unarta, I.S., Cao, S., Goonetilleke1, E.C., Huang, X.*, “Markov state models to study the functional dynamics of proteins in the wake of machine learning”, J. Am. Chem. Soc. Au, 1(9), 1330-1341, (2021)
• Xu, X., Zhang, L.*, Chu, J.T.S., Wang, Y., Chin, A.W.H., Chong, T.H., Dai, Z., Poon, L.L.M., Cheung P.P.H.*, Huang, X.* “A Novel Mechanism of Enhanced Transcription Activity and Fidelity for Influenza A Viral RNA-dependent RNA Polymerase”, Nucleic Acids Res., 49(15), 8796-8810, (2021)
• Oh, J., Shin, J., Unarta, I.S., Wang, W., Feldman, A.W., Karadeema, R.J., Xu, L., Chong, J., Krishnamurthy, R., Huang, X., Romesberg, F.E., Wang, D., “Transcriptional processing of an unnatural base pair by eukaryotic RNA polymerase II”, Nature Chemical Biology, 17, 906–914, (2021)
• Zhu, L., Jiang, H., Cao, S., Unarta, I.C., Gao, X.”, Huang, X.* “Critical role of backbone coordination in the mRNA recognition by RNA induced silencing complex”, Communications Biology, 4:1345, (2021)
• Unarta, I.C., Konovalov, K.A., Wang, X., Suarez, G.D., Huang, X.* “Molecular Dynamics Simulations and Kinetic Network Models Elucidate RNA Polymerase Transcription Elongation Mechanisms“, Chapter 10, Pages 220-244, Book: “RNA Polymerases as Molecular Motors: On the Road: Edition 2”, Editors: Landick, R., Strick., T., Wang, J., Publisher: Royal Society of Chemistry, (2021)
• Yuan, C., Wang, Goonetilleke, E.C., Unarta, I.S., Huang, X.*, “Incorporation Efficiency and Inhibition Mechanism of 2’-Substituted Nucleotide Analogs against SARS-CoV-2 RNA-dependent RNA polymerase”, Phys. Chem. Chem. Phys., 23, 20117 – 20128, (2021)
  – Selected as 2021 HOT PCCP article
• Konovalov, K.A., Wang, W., Wang, G., Goonetilleke, E.C., Gao, X., Wang, D., Huang, X.*, “Comprehensive mechanism for 5-carboxylcytosine induced transcriptional pausing revealed by Markov state models”, J. Biol. Chem., 296, 100735, (2021)
• Wang, Y., Yuan, C., Xu, X., Chong, T.H., Zhang, L., Cheung P.P.H.*, Huang, X.* “The mechanism of action of T-705 as a unique delayed chain terminator on influenza viral polymerase transcription”, Biophysical Chemistry,277, 106652, (2021)
• Liu, Z., Li, C., Goonetilleke, E.C., Cui, Y., Huang, X.* “Role of Surface Templating on Ice Nucleation Efficiency on a Silver Iodide Surface”, J. Phys. Chem. C, 125 (34), 18857-18865, (2021)
• Unarta, I.S., Xu, J., Shang, Y., Cheung, H.P., Zhu, R., Chen, X., Cao, S., Cheung, P.P.H., Bierer, D., Zhang, M.*, Huang, X.*, Li, X.* “Entropy of Stapled Peptide Inhibitors in Free State is the Major Contributor to the Improvement of Binding Affinity”, RSC Chem. Biol., 2, 1274-1284, (2021)
• Quinn, T., Steussy, C.N.; Haines, B.E., Lei, J.; Wang, W.; Sheong, F. K., Cynthia V.S., Huang, X., Norrby, P., Helquist, P., Wiest, O. “Microsecond Timescale Simulations at the Transition State of PmHMGR Predict Remote Allosteric Residues”, Chemical Science, 12, 6413-6418, (2021)
• Wang, X., Unarta, I.C., Cheung P.P.H., Huang, X.* “Elucidating Molecular Mechanisms of Functional Conformational Changes of Proteins via Markov State Models”, Curr. Opin. Struct. Biol, 67, 69-77, (2021)
• Zhang, L.*, Zhang, D., Yuan, C., Wang, X., Li, Y., Jia, X., Gao, X., Yen, H.-L., Cheung, P.*, Huang, X.*, “Role of 1′-Ribose Cyano Substitution for Remdesivir to Effectively Inhibit both Nucleotide Addition and Proofreading in SARS-CoV-2 Viral RNA Replication”, Phys. Chem. Chem. Phys., 23, 5852-5863, (2021), bioRxiv

2020

• Peng, S., Wang, X., Zhang L.*, He, S., Zhao, X.S, Huang, X.*, Chen, C.* “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)
• Cao, S., Montoya-Castillo, Andres., Wang, W., Markland, T.*, Huang, X.*, “On the Advantages of Exploiting Memory in Markov State Models for Biomolecular Dynamics”, J. Chem. Phys.,153, 014105, (2020)
• Cheung, P., Jiang, B., Booth, G.T., Chong, T.H., Unartar, I.C., Wang, Y., Suarez, G.D., Wang, J.*, Lis, J.T.*, Huang, X.*, “Identifying Transcription Error-Enriched Genomic Loci Using Nuclear Run-On Circular-Sequencing Coupled with Background Error Modeling”, J. Mol. Biol., 432(13), 3933-3949, (2020)
• Choy, K., Wong, A., Kaewpreedee, P., Sia, S., Chen, D., Hui, K., Chu, D., Chan, M., Cheung, P., Huang, X., Peiris, M., Yen, H-L, “Remdesivir, lopinavir, emetine, and homoharringtonine inhibit SARS-CoV-2 replication in vitro”, Antiviral Research, 178: 104786, (2020)
• Pan, C., Liu, C., Peng, J., Ren, P.*, Huang, X.*, “Three-site and Five-site Fixed-charge Water Models Compatible with AMOEBA Force Field”, J. Comput. Chem., 41:1034–1044, (2020)

2019

• Lam, J.H., Li, Y., Zhu, L., Umarov, R., Jiang, H., Heliou, A., Sheong, F.K., Liu, T., Long, Y., Li, Y., Fang, L., Altman, R., Chen, W., Huang, X.*, Gao, X.*, “A deep learning framework to predict binding preference of RNA constituents on protein surface”, Nature Communications, 10, 4941, (2019)

         – Recommended by Faculty of 1000

• Tse,C.K.M., Xu, J., Xu, L., Sheong, F.K., Wang, S., Chow, H.Y., Gao, X., Li, X., Cheung, P.P.H.*, Wang, D.*, Zhang, Y.*, Huang, X.*, “Intrinsic Cleavage of RNA Polymerase II Adopts a Nucleobase-independent Mechanism Assisted by Transcript Phosphate “, Nature Catalysis, 2, 228–235, (2019)

           -Highlighted by Natue Middle East

• Lei, J., Sheng, G., Cheung, P.P.H., Wang, S., Li, Y., Gao, X., Zhang, Y.*, Wang, Y.*, Huang, X.*, “Two Symmetric Arginine Residues Play Distinct Roles in Thermus thermophilus Argonaute DNA Guide Strand-mediated DNA Target Cleavage”, Proc. Nat. Acad. Sci. U.S.A., 116(3) 845-853, (2019)
• Cao, S., Konovalov, K., Unarta, I.C., Huang, X.*, “Recent Developments in Integral Equation Theory for Solvation to Treat Density Inhomogeneity at Solute-Solvent Interface”, Advanced Theory and Simulations, 1900049, (2019)
• Zhu, L., Liang, T., Sheong, F.K., Cao, S., Unarta, I.C., Liu, S., Huang, X.*,“TAPS: A Travelling-salesman Based Automated Path Searching Method for Functional Conformational Changes of Biological Macromolecules”, J. Chem. Phys.,150, 124105, (2019), Part of the Special Issue on Markov Models of Molecular Kinetics
• Wang, L., Chen, J., Zeng, X., Cheung, P.P.H., Zheng, X., Shi, X., Ren, L.*, Huang, X.*, Wang, Y.*“Mechanistic Insights and Rational Design of the Versatile Surface with Cells/Bacteria Recognition Capability via Orientated Fusion Peptides”, Adv. Sci., 1801827, (2019)
• Hsieh, S.T., Zhang, L., Ye, D.W., Huang, X.*, Cheng, Y.C.* “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., (2019), DOI: 10.1039/C8FD00205C
• Konovalov, K.A., Pardo-Avila, F., Tse, C.K.M., Oh, J., Wang, D.*, Huang, X.*, “8-oxo-guanine DNA damage induces transcription errors by escaping two distinct fidelity control checkpoints of RNA polymerase II”, J. Biol. Chem., 294 (13), 4924-4933, (2019)

2018

• Zhou, Y., Li, C., Peng, J., Xie, L., Meng, L., Li, Q., Zhang, J., Li, D.X, Li, X.*, Huang, X.*, Li, X*,“DNA-encoded Dynamic Chemical Library and Its Applications in Ligand Discovery”, J. Am. Chem. Soc., 140(46), 15859–15867, (2018)
• Konovalov, K.A., Wang, W.,Huang, X.*, “Conformational selection turns on phenylalanine hydroxylase”, J. Biol. Chem.,293, 19544-19545, (2018)
• Wang, W., Liang, T., Sheong, F.K., Fan, X.*, Huang, X.*,“An Efficient Bayesian Kinetic Lumping Algorithm to Identify Metastable Conformational States via Gibbs Sampling ”, J. Chem. Phys.,149, 072337, (2018), Part of the Special Issue on Enhanced Sampling for Moleuclar Systems
• Peng, J., Wang, W., Yu, Y., Gu, H., Huang, X.*,“Clustering algorithms to Analyze Molecular Dynamics Simulation Trajectories for Complex Chemical and Biological Systems”, Chin. J. Chem. Phys., 31, 404, (2018), Dedicated to the 60th Anniversary of our Alma Mater: USTC, and all the authors obtained B.S. degrees from USTC
• Unarta, I.C., Zhu, L., Tse, K.M., Cheung, P.P.H., Yu, J., Huang, X.*,“Molecular Mechanisms of RNA Polymerase II Transcription Elongation Elucidated by Kinetic Network Models”, Curr. Opin. Struct. Biol, 49, 54-62, (2018)
• Zeng, X., Li, Z.*, Zheng, X., Zhu, L., Sun, Z., Lu, Z., Huang, X.*,“Improving the Productivity of Monodisperse Polyhedral Cages by Rational Design of Kinetic Self-assembly Pathways”, Phys. Chem. Chem. Phys., (2018), DOI:10.1039/C8CP00522B
• Zeng, X., Zhu, L., Zheng, X., Cecchini, M.*, Huang, X.*,“Harnessing Complexity in Molecular Self-Assembly by Computer Simulations”, Phys. Chem. Chem. Phys., 20, 6767-6776 (2018), Part of the themed collection on Complex molecular systems: supramolecules, biomolecules and interfaces
• Molodtsov, V., Sineva, E., Zhang, L., Huang, X., Cashel, M., Ades, S.E., Murakami, K.S. “Allosteric effector ppGpp potentiates the inhibition of transcript initiation by DksA”, Molecular Cell, 69(5), 828–839, (2018)
• Bratkowski, M., Unarta, I.C., Zhu, L., Shubbar, M., Huang, X., Liu, X., “Structural Dissection of an Interaction between Transcription Initiation and Termination Factors Implicated in Promoter−Terminator Crosstalk”, J. Biol. Chem.,293, 1651-1665, (2018)

2017

• Chevalier, A, Silva, D.A., Rocklin, G.J., Hicks, Vergara, Murapa, Bernard, Zhang, L.,…, Huang, X., Jin, R., Wilson, I.A., Fuller, D.H., Baker, D., “Massively parallel de novo protein design for targeted therapeutics”, Nature, 550, 74-79, (2017)
• Jiang, L., Cao, S., Cheung, P.P., Zheng, X., Leung, C.W.T., Peng, Q., Shuai, Z., Tang, B.Z., Yao, S.*, Huang, X.*, “Real-Time Monitoring of Hydrophobic Aggregation Reveals a Critical Role of Cooperativity in Hydrophobic Effect”, Nature Communications, 8, 15639, (2017)
• Zheng, X., Zhu, L., Zeng, X., Meng, L., Zhang, L., Wang, D., Huang, X.*, “Kinetics-Controlled Amphiphiles Self-Assembly Processes”, J. Phys. Chem. Lett., 8, 1798–1803, (2017)
• Wang, W., Cao, S., Zhu, L., Huang, X.*, “Constructing Markov State Models to Elucidate the Functional Conformational Changes of Complex Biomolecules”, WIREs Comput Mol Sci., 8:e1343, (2017)

• Tian, Y., Zeng, X., Li, J., Jiang, Y., Zhao, H., Wang, Y., Huang, .X.*, Li, Z.*, “Achieving Enhanced Cell Penetration of Short Conformationally Constrained Peptides through Amphiphilicity Tuning”, Chemical Science, 8, 7576-7581 (2017)
• Cao, S., Zhu, L., Huang, .X.*, “3DRISM-HI-D2MSA: An improved analytic theory to compute solvent structure around hydrophobic solutes with proper treatment of solute-solvent electrostatic interactions”, Mol. Phys., 116:7-8, 1003-1013, (2018), Part of the Special Issue on Molecular Physics in China
• Meng, L., Sheong, F.K., Zeng, X., Zhu, L., Huang, X.*, “Path Lumping: An Efficient Algorithm to Identify Metastable Path Channels for Conformational Dynamics of Multi-body Systems ”, J. Chem. Phys., 147, 044112, (2017)
• Wen, J., Gu, S., Gao, X., Huang, X.*, Wang, W.*, “Maltose Binding Protein Effectively Stabilizes the Partially Closed Conformation of the ATP-binding Cassette Transporter MalFGK2”, Phys. Chem. Chem. Phys., 19, 9366-9373, (2017)
• Liu, S., Zhu, L.*, Sheong, F.K., Wang, W., Huang, X.*, “Adaptive Partitioning by Local Density-peaks (APLoD): An efficient density-based clustering algorithm for analyzing molecular dynamics trajectories”, J. Comput. Chem. , 38(3):152-160, (2017)
• Zhu, L., Jiang, H., Sheong, F.K., Cui, X.,Wang, Y., Gao, X.*, Huang, X.*, “Understanding the Core of RNA Interference: the Dynamic Aspects of Argonaute-mediated Processes”, Prog. Biophys. Mol. Bio. , 128, 39-46, (2017)
• Zhang, H., Zheng, X., … Huang, X., Wong, K.S., Kwok, R., Sung, H., Williams, I.D., Qin, A., Lam, J.W.Y., Tang, B.Z., “Why do simple molecules with “isolated” phenyl rings emit visible light?”, J. Am. Chem. Soc., 139 (45), 16264–16272, (2017)
• Peng, H., Zheng, X., Han, T., Kwok, R.T.K., Lam, J.W.Y., Huang, X., Tang, B.Z., “Dramatic Differences in Aggregation-Induced Emission and Supramolecular Polymerizability of Tetraphenylethene-Based Stereoisomers”, J. Am. Chem. Soc., 139 (29), 10150, (2017)
• Zhai, Y., Li, N., Jiang, H., Huang, X., Gao, N., Tye, B. “Unique roles played by each of the non-identical MCM subunits in DNA Replication Licensing”, Molecular Cell, 67 (2), 168-179, (2017)

• Zhang, Q., Zheng, X., Kuang, G., Wang, W., Zhu, L., Pang, R., Shi, X., Shang, X., Huang, X., Liu, P., Lin, N., “Single-Molecule Investigations of Conformation Adaptation of Porphyrins on Surfaces”, J. Phys. Chem. Lett., 8, 1241-1247, (2017)
• Li, J., Chen, Y., Deng, Y., Unarta, I.C., Lu, Q., Huang, X., Zhang, M., “Ca2+-induced Rigidity Change of the Myosin VIIa IQ Motif-Single α-Helix Lever Arm Extension”, Structure, 25:1-13, (2017)

2016

• Feng, Y., Zhang, L., Wu, S., Gao, X., Liu, J.*, Huang, X.*, Wang, W.*, “Conformational Dynamics of apo-GlnBP Revealed by Experimental and Computational Analysis”, Angew. Chem. Int. Ed., 55 (45), 13990–13994, (2016)
• Zhang, L., Pardo, F., Unarta, I.C., Cheung, P., Wang, G., Wang, D., and Huang, X.* “Elucidation of the Dynamics of Transcription Elongation by RNA Polymerase II using Kinetic Network Models”, Accounts of Chemical Research, 49 (4), 687–694, (2016)
• Da, L., Pardo, F., Xu, L., Silva, D., Zhang, L., Gao, X., Wang, D.*, Huang, X.*“Bridge Helix Bending Promotes RNA Polymerase II Backtracking Through a Critical and Conserved Threonine Residue”, Nature Communications, 7, 11244, (2016)
• Qiao, Q.*, Qi, R., Wei, G.*, Huang, X.*, “Dynamics of the Conformational Transitions during the Dimerization of an Intrinsically Disordered Peptide: a Case Study on the Human Islet Amyloid Polypeptide Fragment ”, Phys. Chem. Chem. Phys.,18, 29892-29904, (2016)
• Zhu, L., Sheong, F. K., Zeng, X., Huang, X.*, “Elucidating conformational dynamics of multi-body systems by constructing Markov State Models”, Phys. Chem. Chem. Phys., 18, 30228-30235, (2016)

• Zeng, X., Li, B., Qiao, Q., Zhu, L., Lu, Z.-Y.*, Huang, X.*, “Elucidating Dominant Pathways of the Nano-particle Self-Assembly Process”, Phys. Chem. Chem. Phys., 18, 23494-23499, (2016)

• Qiao, Q.*, Zhang, H., Huang, X.*, “Enhancing Pairwise State-transition Weights (EPSW): A New Weighting Scheme in Simulated Tempering that can Minimize Transition Time between a Pair of Conformational States”, J. Chem. Phys., 144, 154107, (2016)
• Zhu, L., Jiang, H., Sheong, F.K., Cui, X., Gao, X., Wang, Y., Huang, X.* “A Flexible Domain-domain Hinge Promotes an Induced-fit Dominant Mechanism for the Loading of Guide-DNA into Argonaute Protein in Thermus Thermophilus”, J. Phys. Chem. B, 120(10), 2709, (2016)
• Zheng, J., Wang, L.*, Zeng, X., Zheng, X., Zhang, Y., Liu, S., Shi, X., Wang, Y., Huang, X.*, Ren, L.*, “Controlling the Integration of Polyvinyl-pyrrolidone onto Substrate by Quartz Crystal Microbalance with Dissipation To Achieve Excellent Protein Resistance and Detoxification”, ACS Appl. Mater. Interfaces, 8(29), 18684-18692, (2016)
• Zhang, L., Jiang, H., Sheong, F.K., Pardo-Avila, F., Cheung, P.P.H., Huang, X.*, “Constructing Kinetic Network Models to Elucidate Mechanisms of Functional Conformational Changes of Enzymes and their Recognition with Ligands”, Methods in Enzymology., 578, 343–371, (2016)
• Zheng, X., Peng, Q.*, Zhu, L., Xie, Y., Huang, X.*, Shuai, Z.*, “Unraveling the aggregation effect on amorphous phase AIE luminogens: A computational study”, Nanoscale, 8, 15173-15180, (2016)

• Tian, Y., Li, J., Zhou, H., Zeng, X., Wang, D., Liu, Q., Niu, X., Huang, X., Xu, N.*, Li, Z.* “Stapling of unprotected helical peptides via photo-induced intramolecular thiolyne hydrothiolation”, Chem. Sci., 7, 3325-3330, (2016).

2015

• Cao, S., Sheong, F.K., Huang, X., “Reference Interaction Site Model with Hydrophobicity induced density Inhomogeneity: An Analytical Theory to Compute Solvation Properties of Large Hydrophobic Solutes in the Mixture of Polyatomic Solvent Molecules”, J. Chem. Phys., 143, 054110, (2015)
• Jiang, H., Sheong, F.K., Zhu, L., Gao, X., Bernauer, J., Huang, X., “Markov State Models Reveal a Two-step Mechanism of miRNA Loading into the Human Argonaute Protein: Selective Binding Followed by Structural Re-arrangement”, PLoS. Comp. Bio., 11(7): e1004404, (2015)
• Zhang, L., Silva, D.A., Pardo-Avila, F., Wang, D., Huang, X., “Structural Model of RNA Polymerase II Elongation Complex with Complete Transcription Bubble Reveals NTP Entry Routes”, PLoS. Comp. Bio., 11(7), e100435, (2015)
• Sheong, F.K., Silva, D.A., Meng, L., Zhao, Y., Huang, X. “Automatic state Partitioning for Multi-body systems (APM): An Efficient Algorithm for Constructing Markov State Models to Elucidate Conformational Dynamics of Multi-body Systems”, J. Chem. Theory Comput., 11 (1), 17–27, (2015)
• Liu, Y., Mu, C., Jiang, K., Zhao, J., Li, Y., Zhang, L., Li, Z., Lai, J., Hu, H., Ma, T., Hu, R., Yu, D., Huang, X., Tang, B., Yan, H. “A Tetraphenylethylene Core-Based 3D Structure Small Molecular Acceptor Enabling Efficient Non-Fullerene Organic Solar Cells”, Adv. Mater., 27(6), 1015-1020, (2015)
• Yu, J., Da, L.T., Huang, X., “Constructing Kinetic Models to Elucidate Structural Dynamics of a Complete RNA Polymerase II Elongation Cycle”, Phys. Bio., 12, 016004, (2015)

2014

• Gu, S., Silva, D.A., Meng, L., Yue, A., Huang, X., “Quantitatively Characterizing the Ligand Binding Mechanisms of Choline Binding Protein using Markov State Model Analysis”, PLoS. Comp. Bio., 10(8):e1003767, (2014)
• Xu, L, Zhang, L., Chong, J., Xu, J., Huang, X., Wang, D., “A Chemical Perspective on Transcriptional Fidelity and Evolution: Asymmetric Recognition of Phosphodiester Linkage by RNA Polymerase II”, Proc. Nat. Acad. Sci. U.S.A., 111, E3269–E3276, (2014)
• Fu, A., Hung, K.W., Huang, H., Gu, S., Shen, Y., Cheng, Ip, F.,, Huang, X, Fu, W.,,Ip, N.Y., “Blockade of EphA4 signaling ameliorates hippocampal synaptic dysfunctions in mouse models of Alzheimer’s disease”, Proc. Nat. Acad. Sci. U.S.A., 111, 9959-9964, (2014)
• Silva, D., Weiss. D., Pardo-Avila, F., Da, L., Levitt, M., Wang, D., Huang, X., “Millisecond Dynamics of RNA Polymerase II Translocation at Atomic Resolution”, Proc. Nat. Acad. Sci. U.S.A., 111, 7665-7670, (2014)

• Zhang, L., Silva, D.A., Yue, A., Zhang, H., Yan, Y., Huang, X., “Dynamic Protein Conformations Preferentially Drive Energy Transfer along Active Chain of the Photosystem-II Reaction Center”, Nature Communications, 5:4170 doi: 10.1038/ncomms5170, (2014)

2013

• Qiao, Q., Bowman, G.R., Huang, X., “Dynamics of an intrinsically disordered protein reveal metastable conformations that potentially seed aggregation”, J. Am. Chem. Soc., 135 (43), 16092–16101, (2013)

• Bowman, G.R., Meng, L., Huang, X., “Quantitative comparison of alternative methods for coarse-graining biological networks ”, J. Chem. Phys., 139, 121905, (2013)
• Yao, Y., Cui, R.Z., Bowman, G.R., Silva, D.A., Sun, J., Huang, X., “Hierarchical Nystrom Methods for Constructing Markov State Models for Conformational Dynamics”, J. Chem. Phys., 138, 174106, (2013)
• Da, L., Pardo-Avila, F., Wang, D., Huang, X., “A Two-State Model for the Dynamics of the Pyrophosphate Ion Release in Bacterial RNA Polymerase”, PLoS. Comp. Bio., 9(4): e1003020, (2013)

• Zhao, Y., Sheong, F.K., Sun, J., Sander, P., Huang, X.“A Fast Parallel Clustering Algorithm for Molecular Simulation Trajectories”, J. Comput. Chem., 34(2), 95-104, (2013)

2012

• Zhang, L., Silva, D.A., Yan, Y.J., Huang, X.“Force Field Development for Cofactors in the Photosystem II ”, J. Comput. Chem., 33 (25), 1969–1980, (2012)
• Liu, J., Su, H., Meng, L., Zhao, Y., Ng, C.Y., Lu, P., Faisal, M., Lam, W.Y., Huang, X., Wu, H., Wong, K.S., Tang, B., “What makes efficient circularly polarised luminescence in the condensed phase: Aggregation-induced circular dichroism and light emission”, Chem. Sci., 3, 2737-2747, (2012)
• Da, L., Wang, D., Huang, X., “Dynamics of Pyrophosphate Ion Release and Its Coupled Trigger Loop Motion from Closed to Open State in RNA Polymerase II”, J. Am. Chem. Soc., 134 (4), 2399, (2012)

• Hong, Y., Meng, L., Chen, S., Leung, C., Da, L., Faisal, M., Silva, D.A., Liu, J., Lam, J., Huang, X., Tang, B., “Monitoring and Inhibition of Insulin Fibrillation by a Small Organic Fluorogen with Aggregation-Induced Emission Characteristics”, J. Am. Chem. Soc., 134 (3), 168, (2012)
• Flores, S., Bernauer, J., Shin, S., Zhou, R., Huang, X., “Multi-scale modeling of macromolecular biosystems”, Briefings in Bioinformatics, 13(4), 395-405, (2012)

2011

• Liu, X., Bushnell D.A., Silva, D.A., Huang, X., and Kornberg R.D. “Initiation Complex Structure and Promoter Proofreading”, Science, 333, 633-637, (2011)
• Silva, D.A., Bowman, G.R., Sosa-Peinado, A., Huang, X., “A Role for Both Conformational Selection and Induced Fit in Ligand Binding by the LAO Protein”, PLoS. Comp. Bio., 7(5), e1002054, (2011)
• Zhuang, W., Cui, R.Z., Silva, D.A., Huang, X., “Simulating the T-jump triggered unfolding dynamics of Trpzip2 peptide and its time resolved IR and 2DIR signals using Markov State Model Approach”, J. Phys. Chem. B., 115, 5415-5424, (2011)

2010

• Huang, X.*, Wang, D, Weiss, D.H., Bushnell, D.A., Kornberg, R.D, and Levitt, M.*,“RNA Polymerase II Trigger Loop Residues Stabilize and Position the Incoming Nucleotide Triphosphate in Transcription” Proc. Nat. Acad. Sci. U.S.A., 107, 15745-15750, (2010)

• Wang, D., Zhu, G., Huang, X., Lippard, S.J., “X-ray structure and mechanism of RNA polymerase II stalled at an antineoplastic monofunctional platinum-DNA adduct”,Proc. Nat. Acad. Sci. U.S.A., 107, 9584-9589, (2010).

• Huang, X.*, Yao Y., Sun J., Bowman G.R.,Guibas L., and Carlsson G.. and Pande V.S. “Constructing Multi-resolution Markov State Models(MSMs) to elucidate RNA hairping folding mechanisms”, Proceedings of the Pacific Symposium on Biocomputing, 15, 228-239, (2010)

2003-2009

• Huang, X., Bowman, G. R., Bacallado, S., and Pande, V. S. “Rapid Equilibrium Sampling Initiated from Non-equilibrium Data”, Proc. Nat. Acad. Sci. U.S.A., 106, 19765-19769, (2009)
• Wang D, Bushnell D.A., Huang, X, Westover K.D., Levitt M, and Kornberg R.D. “Structural Basis of Transcription: Backtracked RNA Polymerase II at 3.4 Angstrom Resolution” , Science, 324, 1203-1206, (2009)
• Bowman G.R., Huang, X, Yao Y, Sun J, Carlsson G, Guibas L., Pande V.S. “Structural Insight into RNA Hairpin Folding Intermediates.” J. Am. Chem. Soc., 130, 9676–9678, (2008)
• Huang, X., Bowman, G. R., and Pande, V. S. “Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment.” J. Chem. Phys. 128, 205106, (2008)
• Huang, X., Hagen, M., Kim, B., Friesner, R.A., Zhou, R and Berne, B.J. “Replica Exchange with Solute Tempering: Efficiency in Large Scale Systems” J. Phys. Chem. B. 111, 5405-5410, (2007)
• Huang, X., Margulis, C.J., Li, Y. and Berne, B.J.,“Why is the Partial Molar Volume of CO2 So Small When Dissolved in a Room Temperature Ionic Liquid? Structure and Dynamics of CO2 Dissolved in [Bmim+] [PF6-].”, J. Am. Chem. Soc., 127, 50, 17842-17851 (2005).
• Liu, P., Huang, X., Zhou, R., Berne, B.J., “Observation of a dewetting transition in the collapse of the melittin tetramer”, Nature, 437, 159-162 (2005).
• Huang, X., Zhou, R. and Berne, B.J., “Drying and Hydrophobic Collapse of Paraffin Plated”, J. Phys. Chem. B, 109, 3546-3552 (2005).
• Zhou, R., Huang, X., Margulis, C.J., and Berne, B.J., “Hydrophobic Collapse in Multi-domain Protein Folding”, Science, 305, 1605-1609 (2004).
• Huang, X., Margulis C.J., and Berne, B.J., “Dewetting-induced collapse of hydrophobic particles”, Proc. Nat. Acad. Sci., 100, 21, 11953-11958 (2003).