Xiaowei Zhuang



Howard Hughes Medical Institute Investigator
David B. Arnold Jr. Professor of Science
Professor of Chemistry and Chemical Biology
Professor of Physics


Harvard University
12 Oxford Street, Cambridge, MA 02138











B.S., Physics, University of Science and Technology of China


Ph.D., Physics, University of California, Berkeley


Chodorow Postdoctoral Fellow, Stanford University




David B. Arnold Jr. Professor of Science, Harvard University


Professor, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University


Investigator, Howard Hughes Medical Institute


Associate Professor, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University


Assistant Professor, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University



Selected awards and elected membership


National Academy of Sciences Award in Molecular Biology


Chinese Institute of Engineers USA Distinguished Achievement Award


Member, American Academy of Arts and Sciences


Member, National Academy of Sciences


Fellow, American Physical Society


Fellow, American Association of the Advancement of Science


Raymond & Beverly Sackler International Prize in Biophysics


Max Delbruck Prize in Biological Physics


HHMI collaborative Innovation Award


Coblentz Award


Pure Chemistry Award


Camille Dreyfus Teacher-Scholar Award


Sloan Research Fellowship


Technology Review Worlds Top 100 Young Innovators Award


MacArthur Fellowship


Packard Fellowship for Science and Engineering


CAREER award, National Science Foundation


Searle Scholar


Beckman Young Investigator Award


Young Investigator Award, Office of Naval Research 


Chodorow Postdoctoral Fellowship, Stanford University


Distinguished lectureship


Krimm Lecture, University of Michigan

Harvey Lecture, Harvey Society

Huck Distinguished Lecture, Penn State University

Laureate Lecture, University of Pittsburg

McLean Lecture, Baylor College

Caspar Lecture, Florida State University


Dow Lecture, University of British Columbia

Global Lecture, Peking University


Danny Thomas Lecture, St Jude Research Hospital

Sproul Lecture, Cornell University

Wang Ying-Lai Lecture, University of Texas Medical Branch

Leica Scientific Forum Lectures, California (UCSF, UCLA, UCSD)


Leica Scientific Forum Lectures, Germany (Munich, Heidelberg, Berlin)

Greenfield Lecture, Case Western University

Fredric Fay Lecture, University of Massachusetts School of Medicine

Closs Lecture, University of Chicago

Maggie & Nick DeWolf Public Lecture, Aspen Center for Physics


Director’s WALS Lecture, National Institutes of Health

Magomedov-Shcherbinina Memorial Prize Lecture, University of Rochester


ST Huang Memorial Lecture, Hong Kong University

Brockman Lecture, University of Michigan

Morrison Lecture, Cornell University


Seymour Rothchild Lecture, University of Rochester


Gunnar and Gunnel Kallén Memorial Lecture, Lund University, Sweden

Jean-Francois Lefèvre Lecture in Biophysics, Ecole Supérieure de Biotechnologie de Strasbourg, France 



Editorial Board Positions

Cell (editorial advisory board) 

eLife  (reviewing editorial board) 

Annual Review on Biophysics (Editorial board, associate editor) 

Optical Nanoscopy (editorial advisory board) 

Chemical Physics Letter (editorial advisory board) 

ACS Central Science (editorial advisory board) 

ACS Photonics (editorial advisory board) 

Partial List of Professional Services 

Co-Chair, Cold Spring Harbor Conference on "New Advances in Optical Imaging of Live Cells and 

Organisms" (2011, 2013) 

Chair, American Society of Cell Biology Meeting, Symposium on “Breaking the diffraction barrier” 


Co-Chair, 355 th  Xiangshan Science Conference, “Single-Molecule Imaging, Spectroscopy and 

Manipulation of Biological Systems,” Beijing, 2009 

Co-chair, Gordon Research Conference on “Single Molecule Approaches to Biology” (2008) 

Co-chair, American Chemical Society National Meeting, Symposium on “Single-molecule imaging, 

spectroscopy, and manipulation of biomolecular systems” (2007) 

Co-vice chair, Gordon Research Conference on “Single Molecule Approaches to Biology” (2006) 

Member, NIH College of CSR Reviewers (2010-present) 

NIH Study Section: Review Panel of the NIH Director’s Pioneer Award (2012, 2014), Review panel 

on Nanomedicine Development Centers for the NIH Roadmap Nanomedicine Initiative (2008), 

Interview panel of the NIH Director’s Pioneer Award (2007), Study section on Molecular 

Structure and Function C (2007), Study section on Cell Structure and Function (2006), Study 

section on Nanomedicine Development Centers for the NIH Roadmap Nanomedicine Initiative 

(2005), Study section on Bioanalytical, Engineering, and Chemistry Emphasis (2003)  

External advisory Board, NSF Center for the Physics of Living Cells (CPLC), UIUC 

Scientific Advisory Board, School of Life Sciences, University of Science of Technology of China

Scientific Advisory Board, ICFO – Institute of Photonics Science, Barcelona, Spain 

Pew Scholars National Advisory Committee 

Scientific Advisory Board, Welch Foundation 



G. Zhong, J. He, R. Zhou, D. Lorenzo, H. P. Babcock, V. Bennett, X. Zhuang. Developmental 

mechanism of the periodic membrane skeleton in axons. eLife (DOI: 10.7554/eLife.04581) 

C. Y. Chan, H. Zhao, R. J. Pugh, A. M. Pedley, J. French, S. A. Jones, X. Zhuang, H. Jinnah, T. J. 

Huang, S. J Benkovic. Purinosome formation as a function of the cell cycle.  Proc. Natl. Acad. 

Sci. USA (in press) 

T. Shemesh, R. W. Klemm, F. B. Romano, S. Wang, J. C. Vaughan, X. Zhuang, M. M. Kozlov, T. 

A. Rapoport. A model for the generation and interconversion of ER morphologies.  Proc. Natl. 

Acad. Sci. USA (in press, DOI: 10.1073/pnas.1419997111) 

D. N. Lorenzo, A. Badea, J. Q. Davis, J. Hostettler, J. He, G. Zhong, X. Zhuang,V. Bennett. A 

PIK3C3–Ankyrin-B–Dynactin pathway promotes axonal growth and multiorganelle transport. J. 

Cell Biol 207, 735-752 (2014). 

W. L. Hwang, S. Deindl, B. T. Harada, X. Zhuang. Histone H4 tail mediates allosteric regulation of 

nucleosome remodelling by linker DNA. Nature 512, 213-217 (2014). 

A D. Blunk, Y. Akbergenova, R. W. Cho, J. Lee, U. Walldorf, K. Xu, G. Zhong, X. Zhuang and J. T. 

Littleton. Postsynaptic actin regulates active zone spacing and glutamate receptor apposition 

at the Drosophila neuromuscular junction. Mol. Cell. Neurosci 61, 241-254 (2014). 

S. Wang, J. R. Moffit, G. T. Dempsey, X. S. Xie, X. Zhuang. Characterization and development of 

photoactivatable fluorescent proteins for single-molecule–based superresolution imaging. 

Proc. Natl. Acad. Sci. USA 111, 8452 – 8457 (2014).  

J. -J. Chung, S. -H. Shim, R. A. Everley, S. P. Gygi, X. Zhuang, D. E. Clapham. Structurally 

Distinct Ca2+ Signaling Domains of Sperm Flagella Orchestrate Tyrosine Phosphorylation and 

Motility. Cell 157, 808–822 (2014) 

S. Jia, J. C. Vaughan, X. Zhuang. Isotropic 3D super-resolution imaging with a self-bending point-

spread function. Nat. Photonics 8, 302-306 (2014) 

A. M. Avalos, A. M. Bilate, M.D. Witte, A. K. Tai, J. He, M. P. Frushicheva, P. D. Thill, F. Meyer-

Wentrup, C. S. Theile, A. K. Chakraborty, X. Zhuang, H. L. Ploegh. Monovalent engagement 

of the BCR activates ovalbumin-specific transnuclear B cells. J. Exp. Med. 211, 365-79 (2014) 

K. Xu, G. Zhong, X. Zhuang. Actin, spectrin and associated proteins form a periodic cytoskeleton 

structure in axons. Science 339, 452-456 (2013). 

Y. Doksani, J. Wu, T. de Lange, X. Zhuang. Super-resolution fluorescence imaging reveals TRF2-

dependent t-loop formation. Cell 155, 345-356 (2013). 

S. Deindl, W. L. Hwang, S. K. Hota, T. R. Blosser, P. Prasad, B. Bartholomew, X. Zhuang. ISWI 

remodelers slide nucleosomes with coordinated multi-base-pair entry steps and single-base- 

pair exit steps. Cell 152, 442-452 (2013). 

H. Babcock, J. Moffitt, Y. Zhao, X. Zhuang. Fast compressed sensing analysis for super-resolution 

imaging using L1-homotopy. Optics Express 21, 28583-28596 (2013). 

J. He, E. Sun, M. B. Bujny, D. Kim, M. W. Davidson, X. Zhuang. Dual function of CD81 in 

influenza uncoating and budding. PLoS Pathogen 9, e1003701 (2013). 

S. K. Hota, S. K. Bhardwaj, S. Deindl, Y. C. Lin, X. Zhuang, B. Bartholomew. Nucleosome 

mobilization by ISW2 requires the concerted action of the ATPase and SLIDE domains. Nat. 

Struct. Mol. Biol. 152, 442-452 (2013). 

J.C. Vaughan, G.T. Dempsey, E. Sun, X. Zhuang. Phospine Quenching of Cyanin Dyes as a 

Versatile Tool for Fluorescence Microscopy. J. Am. Chem. Soc. 135, 1197-1200 (2013). 

E. Sun, J. He, X. Zhuang, Live cell imaging of viral entry. Curr Opin Virol. 3, 34-43 (2013). 

A. P. Alivisatos, A. M. Andrews, E. S. Boyden, M. Chun, G. M. Church, K. Deisseroth, J. P. 

Donoghue, S. E. Fraser, J. Lippincott-Schwartz, L. L. Looger, S. Masmanidis, P. L. McEuen, 

A. V. Nurmikko, H. Park, D. S. Peterka, C. Reid, M. L. Roukes, A. Scherer, M. Schnitzer, T. J. 

Sejnowski, K. L. Shepard, D. Tsao, G. Turrigiano, P. S Weiss, C. Xu, R. Yuste, X. Zhuang. 

Nanotools for neuroscience and brain activity mapping. ACS nano 7, 1850-1866 (2013) 

E. Sun, J. He, X. Zhuang. Dissecting the role of COPI complexes on influenza virus infection. J. 

Virol. 87, 2673-2685(2013) 

I. Kim, W. Pan, S. A. Jones, Y. Zhang, X. Zhuang, D. Wu. Clathrin and AP2 are required for 

PtdIns(4,5)P2-mediated formation of LRP6 signalosomes. J. Cell Biol. 200, 419-428 (2013). 

J. Vaughan, S. Jia, X. Zhuang. Ultra-bright Photoactivatable Fluorophores Created by Reductive 

Caging. Nat. Methods 9, 1181-1184 (2012).  

V. Berk, J. C. N. Fong, G. T. Dempsey, O. N. Develioglu, X. Zhuang, J. Liphardt, F. H. Yildiz, S. 

Chu. Molecular Architecture and Assembly Principles of Vibrio cholerae Biofilms. Science 

337, 236-239  (2012). 

S. -H. Shim, C. Xia, G. Zhong, H. P. Babcock, J. C. Vaughan, B. Huang, X. Wang, C. Xu G.-Q. Bi, 

X. Zhuang. Super-resolution fluorescence imaging of organelles in live cells with 

photoswitchable membrane probes. Proc. Natl. Acad. Sci. USA 109, 13978–13983 (2012). 

S. Deindl, X. Zhuang. Monitoring conformational dynamics with single-molecule fluorescence 

resonance energy transfer: Application in Nucleosome Remodeling. Methods Enzymol 513

59–86 (2012) 

H. Babcock, Y. Sigal, X. Zhuang. A high-density 3D localization algorithm for stochastic optical 

reconstruction microscopy. Nanoscopy 1: 6 (2012).  

E. A. Mukamel, H. P. Babcock, X. Zhuang. Statistical deconvolution for super-resolution 

fluorescence Microscopy. Biophys. J. 102, 2391-2400 (2012) 

K. Xu, H. P. Babcock, X. Zhuang. Dual-objective STORM reveals three-dimensional filament 

organization in the actin cytoskeleton. Nat. Methods 9, 185-188 (2012). 

M. Lakadamyali, H. Babcock, M. Bates, X. Zhuang, J. Lichtman. 3D Multicolor Super-Resolution 

Imaging Offers Improved Accuracy in NeuronTracing. PLoS One 7: e30826 (2012) 

M. Bates, G. T. Dempsey, K. H. Chen, X. Zhuang. Multicolor super-resolution fluorescence 

imaging through via multi-parameter fluorophore detection. Chemphyschem 13, 99-107 


G. T. Dempsey, J. C. Vaughan, K. H. Chen, M. Bates, X. Zhuang. Evaluation of fluorophores for 

optimal performance in localization-based super-resolution imaging. Nat. Methods 8, 1027-

1036 (2011). 

J. C. Vaughan, X. Zhuang. New fluorescent probes for Super-resolution imaging. Nat. 

Biotechnol. 29, 880-881 (2011) 

W. Wang, G.W. Li, C. Chen, X. S. Xie, X. Zhuang. Chromosome organization by a nucleoid 

associated protein. Science 333, 1445-1449 (2011).  

E. C. Garner, R. Bernard, W. Wang, X. Zhuang, D. Z. Rudner, T. Mitchison. Circumferential 

Motions of the Cell Wall Synthesis Machinery Drive Cytoskeletal Dynamics in B. subtilis. 

Science 333, 222-225 (2011). 

S. Jones, S.-H. Shim, J. He, X. Zhuang. Fast three-dimensional super-resolution imaging of live 

cells. Nat. Methods 8, 499-505 (2011). 

M. Mihalusova, J. Y. Wu, X. Zhuang. Functional importance of telomerase pseudoknot revealed 

by single-molecule analysis. Proc. Natl. Acad. Sci. USA 108, 20339-20344 (2011). 

B. Huang, H. Babcock, X. Zhuang, Breaking the diffraction barrier: Super-resolution imaging of 

cells. Cell 143, 1047-1058 (2010). 

S. Liu, B. T. Harada, J. T. Miller, S. F. J. Le Grice, X. Zhuang. Initiation complex dynamics direct 

the transitions between distinct phases of early HIV reverse transcription. Nat. Struct. Mol. 

Biol. 17, 1453-1460 (2010) 

A. Dani, B. Huang, J. Bergan, C. Dulac, X. Zhuang. Super-resolution imaging of chemical 

synapses in the brain. Neuron 68, 843-856 (2010) 

M. Wu, B. Huang, M. Graham, A. Raimondi, J. E. Heuser, X. Zhuang, P. De Camilli. Coupling 

between clathrin-dependent endocytic budding and F-BAR-dependent tubulation in a cell-free 

system. Nat. Cell Biol. 12, 902-908 (2010) 

S. Chung, M. Wendeler, J. W. Rausch, G. Beilhartz, M. Gotte,  B. R. O’Keefe, A. Bermingham, J. 

A. Beutler, S. Liu, X. Zhuang, S. F.J. Le Grice. Structure-Activity Analysis of Vinylogous Urea 

Inhibitors of Human Immunodeficiency Virus-Encoded Ribonuclease H. Antimicrob Agents 

Chemother 54, 3913-3921 (2010) 

E. Schuman, X. Zhuang. New technologies, Editorial overview. Curr Opin Neurobiology 20, 608-

690 (2010) 

M. Bates, S. A. Jones, X. Zhuang. Stochastic Optical Reconstruction Microscopy (STORM) -- A 

Method for Superresolution Fluorescence Imaging. Chapter 35 in Imaging: A Laboratory 

Manual. Ed. Rafael Yuste. Cold Spring Harbor Laboratory Press (2010) 

G. Dempsey, W. Wang, X. Zhuang, Fluorescence Imaging at Sub–Diffraction-Limit Resolution with 

Stochastic Optical Reconstruction Microscopy. Pp. 95-127 in Handbook of Single-molecule 

Biophysics (ed. Hinterdorfer P, van Oijen AM), Springer Science and Business Media, New 


T. Blosser, J. Yang, M. Stone, G. Narlikar, X. Zhuang, Dynamics of nucleosome remodeling by 

individual ACF complexes. Nature 462, 1022-1027 (2009)  

G. T. Dempsey, M. Bates, W. E. Kowtoniuk, D. R. Liu, R. Y. Tsien, X. Zhuang. Photoswitching 

mechanism of cyanine dyes. J. Am. Chem. Soc. 131, 18192-18193 (2009) 

M. Bates, B. Huang, M. Rust, G. Dempsey, W. Wang, X. Zhuang. Sub-diffraction-limit Imaging 

with Stochastic Optical Reconstruction Micrscopy (STORM). Nobel Volume on Single 

Molecule Spectroscopy in Chemistry, Springer Publishing (2009).  

J. Wu, M. Stone, X. Zhuang. A Single-molecule assay for telomerase structural-function analysis. 

Nucleic Acid Res. doi:10.1093/nar/gkp1033 (2009)  

J. Vaughan, B. Brandenburg, J. Hogle, X. Zhuang. Rapid actin-dependent viral motility in live cells. 

Biophysical Journal 97, 1647-1656 (2009)  

X. Zhuang. Nano-imaging with STORM. Nat. Photon. 3, 365-367 (2009)  

Huang, M. Bates, X. Zhuang. Super-resolution fluorescence microscopy. Annu. Rev. Biochem. 

78, 993 – 1016 (2009) 

E. Abbondanzieri, X. Zhuang. Concealed enzyme coordination. Nature 457, 392-393 (2009). 

H. M. van der Schaar, M. J. Rust, C. Chen, H. van der Ende-Metselaar, J. Wilschut, X. Zhuang, J. 

M. Smit. Dissecting the cell entry pathway of single Dengue virus particles in living cells. PLoS 

Pathogen 4, e1000244 (2009) 

S. Liu, E. Abbondanzieri, J. W. Rausch, S. F. J. Le Grice, X. Zhuang. Slide into action: dynamic 

shuttling of HIV reverse transcriptase on nucleic acid substrate. Science 322, 1092-1097 


B. Huang, S. Jones, B. Brandenburg, X. Zhuang. Whole cell 3D STORM reveals interactions 

between cellular structures with nanometer-scale resolution. Nat. Meth. 5, 1047 - 1052 (2008). 

M. Bates, B. Huang, X. Zhuang. Super-resolution microscopy by nanoscale localization of photo-

switchable fluorescent probes. Curr. Opin. Chem. Biol. 208, 1-10 (2008) 

C. Chen, X. Zhuang. Epsin1 is a cargo specific adaptor for the clathrin-mediated endocytosis of 

influenza virus. Proc. Natl. Acad. Sci. USA 105, 11790-11795 (2008) 

J. Zheng, X. Zhuang. Luminescent and Raman active silver nanoparticles with polycrystalline 

structure. J. Am. Chem. Soc. 130, 10472-10473 (2008) 

E. Abbondanzieri, G. Bokinsky, J. W. Rausch, J. X. Zhang, S. F. J. Le Grice, X. Zhuang. Dynamic 

binding orientations direct activity of HIV reverse transcriptase. Nature 453, 184-189 (2008). 

B. Huang, W. Wang, M. Bates, X. Zhuang. Three-dimensional super-resolution imaging by 

stochastic optical reconstruction microscopy. Science 319, 810-813 (2008). 

M. Bates, B. Huang, G. Dempsey, X. Zhuang. Multicolor super-resolution imaging with photo-

switchable fluorescent probes. Science 317, 1749-1753 (2007). 

S. Liu, G. Bokinsky, N. G. Walter, X. Zhuang. Dissecting the multi-step reaction pathway of an 

RNA enzyme by single-molecule kinetic fingerprinting. Proc. Natl. Acad. Sci. USA 104

12634-12639 (2007). 

M. D. Stone, M. Mihalusova, C. M. O’Connor, R. Prathapam, K. Collins, X. Zhuang. Stepwise 

protein-mediated RNA folding directs assembly of telomerase ribonucleoprotein. Nature 446

458-461 (2007). 

B. Brandenburg, L. Y. Lee, M. Lakadamyali, M. J. Rust, X. Zhuang, and J. M. Hogle. Imaging 

poliovirus entry in live cells. PLoS Biol. 5, 1543-1555 (2007).  

B. Brandenburg, X. Zhuang. Virus trafficking – learning from single-virus tracking. Nat. Rev. 

Microbiol. 5, 197-208 (2007). 

 M. J. Rust, M. Lakadamyali, B. Brandenburg, and X. Zhuang. Single-virus tracking in live cells. In 

Single Molecule Techniques Ed. P.S. Selvin and T.Ha (Cold Spring Harbor Laboratory Press). 

Y. Zhou, X. Zhuang. Kinetic analysis of sequential multi-step reactions. J. Phys. Chem. B, 111

13600-13610, 2007 (2007). 

H. M. van der Shaar, M. J. Rust, B. Waarts, H. van der Ende Metselaar, R. J. Kuhn, J. Wilschut, X. 

Zhuang, J. M. Smit. Characterization of the early events in Dengue virus cell entry by 

biochemical assays and single-virus tracking. J. Virol., 81, 12019-12028 (2007). 

C. K. Payne, S. Jones, C. Chen, X. Zhuang. Internalization and trafficking of cell surface 

proteoglycans and proteoglycan binding ligands. Traffic 8, 389-401 (2007). 

Y. Zhou and X. Zhuang. Robust reconstruction of the rate constant distribution using the phase 

function method. Biophys. J. 91, 4045-4053 (2006). 

M. J. Rust, M. Bates, X. Zhuang. Sub-diffraction-limit imaging by stochastic reconstruction optical 

microscopy (STORM). Nat. Meth. 3, 793-795 (2006). 

G. Bokinsky, L. G. Nivon, S. Liu, G. Chai., M. Hong, K. M. Weeks, X. Zhuang. Two distinct binding 

mode of a protein cofactor with its target RNA. J. Mol. Biol. 361, 771-784 (2006). 

M.  Lakadamyali,  M.  J.  Rust,  X.  Zhuang.  Ligands  for  clathrin-mediated  endocytosis  are 

differentially sorted into distinct populations of early endosomes. Cell 124, 997-1009 (2006). 

X. Zhuang. Single-molecule RNA Science. Annu.  Rev.  Biophys.  Biomol.  Struct.  34, 399-414 


G. Bokinsky, X. Zhuang. Single-molecule RNA folding. Acct.  Chem. Res. 38, 566-573 (2005).

M. Bates, T. R. Blosser, X. Zhuang. Short-range spectroscopic ruler based on a single-molecule 

optical switch. Phys. Rev. Lett. 94, 108101 (2005). 

X. Zhuang. Unraveling DNA condensation by optical tweezers. Science 305, 188-190 (2004).  

M. Lakadamyali, M. J. Rust, X. Zhuang. Endocytosis of influenza viruses. Micro.  Infect. 6, 929-

936 (2004).  

M.  J.  Rust,  M.  Lakadamyali,  F.  Zhang,  X.  Zhuang.  Assembly  of  endocytic  machinery  around 

individual influenza viruses during viral entry. Nat. Struct. Mol. Biol. 11, 567-573 (2004). 

F. Patolsky, G. Zheng, O. Hayden, M. Lakadamyali, X. Zhuang, C. M. Lieber. Electrical detection 

of single viruses. Proc. Natl. Acad. Sci. USA 101, 14017-14022 (2004). 

H. P. Babcock, C. Chen, X. Zhuang. Using single particle-tracking to study nuclear trafficking of 

viral genes. Biophys. J. 87, 2749-2758 (2004). 

D.  Rueda,  G.  Bokinsky,  M.  M.  Rhodes,  M.  J.  Rust,  X.  Zhuang,  N.  G.  Walter.  Single-molecule 

enzymology of RNA: Essential functional groups impact catalysis from a distance. Proc. Natl. 

Acad. Sci. USA 101, 10066-10071 (2004). 

M. Lakadamyali, M. J. Rust, H P. Babcock, X. Zhuang. Visualizing infection of individual influenza 

viruses. Proc. Natl. Acad. Sci. USA 100, 9280-9285 (2003). 

G. Bokinsky, D. Rueda, V. K. Misra, A. Gordus, M. M. Rhodes, H. P. Babcock, N. G. Walter, X. 

Zhuang. Single-molecule transition-state analysis of RNA folding. Proc. Natl. Acad. Sci. USA 

100, 9302-9307 (2003). 

X. Zhuang and M. Rief. Single-molecule folding. Curr. Opin. Struct. Biol. 13, 88-97 (2003).  

L.  E.  Bartley,  X.  Zhuang,  R.  Das,  S.  Chu,  D.  Herschlag.  Exploration  of  the  transition  state  for 

tertiary structure formation between an RNA helix and a large structured RNA. J.  Mol.  Biol. 

328, 1011-1026 (2003). 

X. Zhuang, H. Kim, M. Pereira, H. Babcock, N. Walter, S. Chu.  Correlating structural dynamics 

and function in single ribozyme molecules. Science 296, 1473-1476 (2002). 

R. Russell, X. Zhuang, H. Babcock, I. S. Millett, S. Doniach, S. Chu, D. Herschlag. Exploring the 

folding landscape of a structured RNA. Proc. Natl. Acad. Sci. USA 99, 155-160 (2002). 

X. Zhuang, L. Bartley, H. Babcock, R. Russell, T. Ha, D. Herschlag, S. Chu. A single-molecule 

study of RNA catalysis and folding. Science 288, 2048-2051 (2000). 

X.  Zhuang,  T.  Ha,  H.  Kim,  T.  Centner,  S.  Labeit,  S.  Chu.  Fluorescence  quenching:  a  tool  for 

single-molecule protein-folding study. Proc. Natl. Acad. Sci. USA 97, 14241-14244 (2000). 

T. Ha, X. Zhuang, H. Kim, J. Orr, J. Williamson, S. Chu. Ligand-induced conformational changes 

of single RNA molecules. Proc. Natl. Acad. Sci. USA 96, 9077-9082 (1999). 

S.-C. Hong, M. Oh-e, X. Zhuang, Y. R. Shen, J. J. Ge, F. W. Harris, S. Z. D. Cheng. Orientation of 

side chains and adsorbed liquid crystal molecules on a rubbed polyimide surface studied by 

optical harmonic generation. Phys. Rev. E 63, 0517061-7 (2001). 

J. J. Ge, C. Y. Li, G.I. Xue, I. K. Mann, S. Z. D. Cheng, J. Z. Zhang, D. Zhang, S. Wang, F. W. 

Harris,  S.-C.  Hong,  X.  Zhuang,  Y.  R.  Shen.  Rubbing-induced  molecular  reorientation  on  an 

alignment  surface  of  an  aromatic  polyimide  containing  cyanobiphenyl  side  chains.  J.  Am. 

Chem. Soc. 123, 5768-5776 (2001). 

X.  Wei,  X.  Zhuang,  D.  Kim,  S.-C.  Hong,  T.  Goto,  and  Y.  R.  Shen.  Vibrational  spectroscopy  of 

rubbed polymer surfaces. Mole. Cryst. Liq. Cryst. 358, 103-108 (2001). 

X.  Wei,  S.  Hong,  X.  Zhuang,  T.  Goto,  Y.  R.  Shen.  Nonlinear  optical  studies  of  liquid  crystal 

alignment on a rubber polyvinyl alcohol surface. Phys. Rev. E 62, 5160-5172, (2000).

X. Wei, X. Zhuang, S. Hong, T. Goto, Y. R. Shen. Sum-Frequency vibrational spectroscopic study 

of a rubbed polymer surface. Phys. Rev. Lett. 82, 4256-4259 (1999). 

X. Zhuang, P. B. Miranda, D. Kim, Y. R. Shen. Mapping molecular orientation and conformation at 

interfaces by surface nonlinear optics. Phys. Rev. B 59, 12632-12640 (1999). 

T. Qian, X. Zhuang, Y. R. Shen. Surface-monolayer-induced bulk alignment of liquid crystals: from 

nematic to smectic-a phase. Phys. Rev. E 59, 1873-1879 (1999). 

X.  Zhuang,  R.  Muenster,  M.  Jarasch,  Y.  R.  Shen.  “Dye-induced  enhancement  of  optical 

nonlinearity  in  liquid  crystals  and  ordinary  liquids.  Mole.  Cryst.  Liq.  Cryst.  321,  165-172 


J. J. Ge, G.Xue, K. W. McCreight, S. Wang, F. W. Harris, S. Z. D. Cheng, X. Zhuang, S. Hong, Y. 

R. Shen. Surface studies of polyimide thin films via surface enhanced Raman scattering and 

second harmonic generation. Macromol. Rapid Comm. 19, 619-623 (1998). 

R.  Muenster,  M.  Jarasch,  X.  Zhuang,  Y.  R.  Shen.  Enhanced  optical  kerr  effect  of  dye-doped 

isotropic liquid. Phys. Rev. Lett. 78, 42-45 (1997). 

X.  Zhuang  and  Y.  R.  Shen.  The  application  of  nonlinear  optics  to  the  study  of  polymers  at 

interfaces. Trends Polym. Sci. 4, 258-264 (1996).  

A.  Le  Calvez,  S.  Montant,  E.  Freysz,  A.  Ducasse,  X.  Zhuang,  Y.  R.  Shen.  Ultrafast  orientation 

dynamics of liquid crystals in smectic phase. Chem. Phys. Lett. 258, 620-625 (1996). 

X. Zhuang, H. S. Lackritz, and Y. R. Shen. Photo-isomerization of polymer monolayers and multi-

layers on water. Chem. Phys. Lett. 246, 279-284 (1995). 

X. Zhuang, D. Wilk, L. Marrucci, and Y. R. Shen. Orientation of amphiphilic molecules on polar 

substrates. Phys. Rev. Lett. 75, 2144-2147 (1995). 

X.  Zhuang,  L.  Marrucci,  D.  Johannsmann,  and  Y.  R.  Shen.  Dependence  of  liquid  crystal  bulk 

alignment on its surface monolayer. Mole. Cryst. Liq. Cryst. 262, 35-43 (1995). 

X.  Zhuang,  L.  Marrucci,  and  Y.  R.  Shen.  Surface-monolayer-induced  bulk  alignment  of  liquid 

crystals. Phys. Rev. Lett. 73, 1513-1516 (1994).