Taekjip Ha
Professor of Physics and Biophysics
University of Illinois at Urbana-Champaign
Department of Physics, 1110 West Green Street, Urbana, IL 61801
Tel: 217-265-0717 • Fax: 217-244-7187
e-mail: tjha@uiuc.edu

• 1996 Ph.D. in physics, University of California at Berkeley, Berkeley, CA 94720
  Thesis: Fluorescence Spectroscopy of Single Molecules at Room Temperature and Its Applications
  (advisors: Shimon Weiss and Daniel Chemla)
• 1991 M.A. in physics, University of California at Berkeley, Berkeley, CA 94720
• 1990 B.S. in physics, Seoul National University, Seoul, Republic of Korea

• 08/2007–present: Professor, Department of Physics and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign
• 01/2006–present: Affiliate, Beckman Institute, University of Illinois at Urbana-Champaign
• 09/2005–present: Investigator, Howard Hughes Medical Institute
• 05/2005–present: Affiliate, Dept of Medical Biochemistry, College of Medicine at University of Illinois at Urbana-Champaign
• 01/2005–present: Faculty Member of the Precision Proteomics Research Theme, Institute for Genomic Biology, University of Illinois at Urbana-Champaign
• 08/2004–8/2007: Associate Professor, Dept of Physics and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign
• 01/2004–present: Affiliate, Department of Chemistry, University of Illinois at Urbana-Champaign
• 08/2000–07/2004: Assistant Professor, Dept of Physics and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign
• 01/1998–08/2000: Post-doctoral Fellow (advisor: Steven Chu), Physics Dept, Stanford Univ., Stanford, CA 94305
• 1997 (summer): Visiting Scientist, Technical University of Denmark, Lyngby, Denmark
• 01/1997–12/1997: Post-doctoral Fellow (advisors: Shimon Weiss and Daniel Chemla), Materials Sciences Div., Lawrence Berkeley National Laboratory, Berkeley, CA 94720

RESEARCH INTERESTS

RECENT TEACHING EXPERIENCE

• College Physics, E&M & Modern, Spring 2007
• Physical Biology: From Single Molecules to Systems Biology, Spring 2006
• Physics 371: Light, Spring 2003, Fall 2004, Spring 2005
• General Physics (Electromagnetism, Light, X-Rays, Atoms, Relativity), Fall 2000, Fall 2001, Spring 2002
• Advisor for 4 master students; 18 doctoral students; 22 post-doctoral fellows, 2000-present

• 2007 Michael and Kate Barany Award for Young Investigators, Biophysical Society
• 2005 Fellow, American Physical Society
• 2005 Howard Hughes Medical Institute Investigator
• 2004 Participant: Japanese-American National Academy of Engineering Frontiers of Engineering meeting
• 2003 Alfred P. Sloan Fellow
• 2003 Xerox Faculty Research Award, UIUC
• 2003 Beckman Fellow at Center for Advanced Studies, UIUC
• 2003 Cottrell Scholar, Research Corporation
• 2002 Fluorescence Young Investigator Award, Biophysical Society
• 2002 NSF CAREER Award
• 2002 Participant: German-American National Academy of Sciences Frontiers of Science meeting
• 2001 Searle Scholars Award
• 2001 Research Innovation Award, Research Corporation
• 2001 Outstanding Young Researcher Award, AKPA
• 1992–1995 Korean Government Scholarship
• 1990 University Fellowship, University of California, Berkeley
• 1990–1996 Oversea Graduate Fellow, KFAS
• 1990 Graduated with High Honors, Seoul National University
• 1987–1990 Undergraduate Fellow, KFAS

American Physical Society, Biophysical Society

• Nature Physics, Physical Review Letters, Cell, EMBO Journal, Biophysical Journal, Nature, Science, Applied Physics Letters, Review of Scientific Instruments, Nature Structural & Molecular Biology, Nature Cell Biology, Nature Chemical Biology, Nature Methods, Molecular Cell, Structure, Journal of Molecular Biology, Journal of Biomedical Optics, Journal of Physical Chemistry A and B, Macromolecules, Nucleic Acids Research, PNAS, Analytical Biochemistry, Journal of American Chemical Society, Journal of Chemical Physics, Langmuir, Physical Review E, Biochemistry, Analytical Chemistry, Chemical Physics Letters, Angewandte Chemie, Manuscript Reviewer, 2000-present.
• NSF, DOE, NIH, PRF, Research Corp., FOM, Human Frontier Fdn., and Volkswagen Fdn., Proposal Reviewer, 2000-present.
• Preliminary Exam Committee, Member, Spring 2001-present.
• Thesis Committee, Advisor, Summer 2001-present.
• Biological Physics Seminar, Organizer, Spring 2001-present.
• Search Committee, Theoretical Biophysics Faculty, Member, Fall 2003-present.
• NIH Study Session (MSF-C), Member, July 2006-June 2010.
• Executive Committee, Center for Biophysics and Computational Biology, UIUC, Member, 2005-present.
• Executive Committee, NIH Molecular Biophysics Training Grant, UIUC, Member, 2005-present.
• Editorial Board of Physical Biology, Member, October 2006-present.
• Editorial Board of Structure, Member, October 2006-present.
• Committee to assist the National Institute of General Medical Sciences (NIGMS) develop a five-year strategic plan, Member, April 12-13, 2007.

PUBLICATIONS

Publications based on work done prior to moving to the University of Illinois

1. T. Ha, Th. Enderle, D.F. Ogletree, D.S. Chemla, P. Selvin, and S. Weiss, “Probing the interaction between two single molecules: Fluorescence resonance energy transfer between a single donor and a single acceptor ,” Proc. Natl. Acad. Sci. U.S.A. 93, 6264 (1996).
2. T. Ha, Th. Enderle, D.S. Chemla, P. R. Selvin, and S. Weiss, “Single molecule dynamics studied by polarization modulation,” Phys. Rev. Lett. 77, 3979 (1996).
3. T. Ha, D.S. Chemla, Th. Enderle, and S. Weiss, “Single molecule spectroscopy with automated positioning,” Appl. Phys. Lett. 70, 782 (1997).
4. Th. Enderle, T. Ha, D.S. Chemla, C. Magowan, and S. Weiss, “Surface specific mapping and co-localization of malarial and host proteins in red-blood-cell membrane by dual-color near-field scanning optical microscopy,” Proc. Natl. Acad. Sci. U.S.A. 94, 520 (1997).
5. T. Ha, Th. Enderle, D.S. Chemla, and S. Weiss, “Dual-molecule spectroscopy: molecular rulers for the study of biological macromolecules,” IEEE JSTQE 2, 1115 (1996).
6. T. Ha, Th. Enderle, P. R. Selvin, D.S. Chemla, and S. Weiss, “Quantum jumps of single molecules at room temperature,” Chem. Phys. Lett. 271, 1 (1997).
7. T. Ha and D.S. Chemla, Th. Enderle, and S. Weiss, “Strategy for room temperature spectroscopy of single molecules,” Bioimaging 5, 99 (1997).
8. T. Ha, J. Glass, Th. Enderle, D.S. Chemla, and S. Weiss, “Hindered rotational diffusion and rotational jumps of single molecules,” Phys. Rev. Lett. 80, 2093 (1998).
9. Th. Enderle, T. Ha, D.S. Chemla, and S. Weiss, “Near-field fluorescence microscopy of cells,” Ultramicroscopy 71, 303 (1998).
10. U. D. Keil, T. Ha, J. R. Jensen, J. M. Hvam, “Femtosecond tunneling response of surface plasmon polaritons,” Appl. Phys. Lett. 72, 3074 (1998).
11. U. Banin, M. Bruchez, A. P. Alivisatos, T. Ha, S. Weiss, and D.S. Chemla, “Evidence for a thermal contribution to emission intermittency in single CdSe/CdS core/shell nanocrystals,” J. Chem. Phys. 110, 1195 (1999).
12. T. Ha, A. Y. Ting, J. Liang, W. B. Caldwell, A. A. Deniz, D.S. Chemla, P. G. Schultz, and S. Weiss, “Single molecule fluorescence spectroscopy of enzyme conformational dynamics and cleavage mechanism,” Proc. Natl. Acad. Sci. U.S.A. 96, 893 (1999).
13. A. A. Deniz , M. Dahan, J. Grunwell, T. Ha, A. E. Faulhaber, D. S. Chemla, S. Weiss, and P. G. Schultz, “Single pair FRET on freely diffusing molecules: observation of Förster distance dependence and sub-populations,” Proc. Natl. Acad. Sci. U.S.A. 96, 3670 (1999).
14. T. Ha, A. Y. Ting, J. Liang, A. A. Deniz, D.S. Chemla, P. G. Schultz, and S. Weiss, “Temporal fluctuations of fluorescence resonance energy transfer between two dyes conjugated to a single protein,” Chem. Phys. 247, 107 (1999).
15. M. Dahan, A. A. Deniz, T. Ha, D. S. Chemla, P. G. Schultz, and S. Weiss, “Ratiometric Measurement and Identification of Single Diffusing Molecules,” Chem. Phys. 247, 85 (1999).
16. T. Ha, T. A. Laurence, D. S. Chemla, and S. Weiss, “Polarization Spectroscopy of Single Fluorescent Molecules,” J. Phys. Chem. B 103, 6839 (1999).
17. T. Ha, X. Zhuang, H. D. Kim, J. W. Orr, J. R. Williamson, and S. Chu, “Ligand induced Conformational Changes observed on Single RNA Molecules,” Proc. Natl. Acad. Sci. U.S.A. 96, 9077 (1999).
18. X. Zhuang, L. Bartley, H. P. Babcock, R. Russell, T. Ha, D. Herschlag, and S. Chu, “A Single Molecule Study of RNA Catalysis and Folding,” Science 288, 2048 (2000).
19. X. Zhuang, T. Ha, H. D. Kim, T. Centner, S. Labeit, and S. Chu, “Fluorescence quenching: A tool for single-molecule protein-folding study,” Proc. Natl. Acad. Sci. USA 97, 14241 (2000).
20. H. D. Kim, G. U. Nienhaus, T. Ha, J. W. Orr, J. R. Williamson, and S. Chu, “Mg2+ dependent conformational change of RNA studied by fluorescence correlation on immobilized single molecules,” Proc. Natl. Acad. Sci. USA 99, 4284-4289 (2002).
21. J. Johnson, T. Ha, S. Chu, and S. Boxer, “Initial steps in supported bilayers formation probed by single vesicle assays,” Biophysical J. 83, 3371 (2002).

1. T. Ha, “Single Molecule Fluorescence Resonance Transfer,” Methods 25, 78 (2001).
2. T. Ha, “Single molecule fluorescent methods for nucleic acid studies,” Current Opinion in Structural Biology 11, 287 (2001).
3. T. Ha*, I. Rasnik, W. Cheng, H. P. Babcock, G. Gauss, T. M. Lohman, and S. Chu, “Initiation and re-initiation of DNA unwinding by the Escherichia coli Rep helicase,” Nature 419, 638-641 (2002) *single corresponding author.
4. S.A. McKinney, A. C. Declais, D. M. J. Lilley, and T. Ha, “Structural dynamics of individual Holliday junctions,” Nature Structural Biology 10, 93-97 (2003).
5. T. Ha and J. Xu and, “Photo-destruction intermediates probed by an adjacent reporter molecule,” Phys. Rev. Lett. 90, 223002 (2003)
6. Yildiz, J. Forkey, S.A. McKinney, T. Ha, Y. Goldman and P. R. Selvin, “Myosin V walks hand over hand: Single fluorophore imaging with 1.5 nanometer localization,” Science 300, 2061-2065 (2003)
7. M. C. Murphy, I. Rasnik, W. Cheng, T. M. Lohman and T. Ha, “Probing single stranded DNA conformational flexibility using fluorescence spectroscopy,” Biophysical J. 86, 2530-2537 (2004).
8. E. Tan, T. J. Wilson, M. K. Nahas, R. M. Clegg, D. M. J. Lilley and T. Ha, “A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate,” Proc. Natl. Acad. Sci. USA. 100, 9308 (2003)
9. J.B. Robbins, M. C. Murphy, B.A. White, R.I. Mackie, T. Ha and I. K. O. Cann, “Functional analysis of multiple single-stranded DNA-binding proteins from Methanosarcina acetivorans and their effects of DNA synthesis by PolBI,” J. of Biological Chemistry 279, 6315-26 (2004).
10. S. A. McKinney, E. Tan, T. J. Wilson, M. K. Nahas, A. C. Declais, R. M. Clegg, D. M. J. Lilley and T. Ha, “Single molecule studies of DNA and RNA four-way junctions,” Biochemical Society Transactions 32, 41-45 (2004).
11. S. Hohng, E. Tan, T. J. Wilson, R. M. Clegg, D. M. J. Lilley and T. Ha, “Conformational flexibility of four-way junctions in RNA,” J. of Molecular Biology 336, 69-79 (2004).
12. I. Rasnik, S. Myong, W. Cheng, T. M. Lohman and T. Ha, “DNA-binding orientation and domain conformation of the E. coli Rep helicase monomer bound to a partial duplex junction: Single-molecule studies of fluorescently labeled enzymes,” J. of Molecular Biology 336, 395-408 (2004).
13. B. C. Stevens and T. Ha, “Discrete and heterogeneous rotational dynamics of single membrane probe dyes in gel phase supported bilayers” J. of Chemical Physics 120, 3030-3039 (2004).
14. S. Hohng and T. Ha, “Near-complete suppression of quantum dot blinking in ambient conditions,” J. of American Chemical Society 126, 1324-1325 (2004).
15. C. Joo, S. A. McKinney, D. M. J. Lilley and T. Ha, “Exploring rare conformational species and ionic effects in DNA Holliday junctions using single-molecule spectroscopy,” J. of Molecular Biology 341, 739-751 (2004).
16. T. Ha, “Structural dynamics and processing of nucleic acids revealed by single molecule spectroscopy,” Biochemistry 43, 4055-4063 (2004).
17. M. P. Gordon, T. Ha and P. R. Selvin, “Single Molecule High Resolution Imaging with Photobleaching,” Proc. Natl. Acad. Sci. USA 101, 6462-6465 (2004).
18. S. Hohng, C. Joo and T. Ha, “Single-molecule Three-color FRET,” Biophysical J. 87, 1328-1337 (2004).
19. M. K. Nahas, T. J. Wilson, S. Hohng, K. Jarvie, D. M. J. Lilley and T. Ha, “Observation of internal cleavage and ligation reactions of a ribozyme,” Nature Structural & Molecular Biology 11, 1107-1113 (2004).
20. B. Okumus, T. J. Wilson, D. M. J. Lilley and T. Ha, “Vesicle encapsulation studies reveal that single molecule ribozyme heterogeneities are intrinsic,” Biophysical J. 87, 2798-2806 (2004).
21. J. Yu, T. Ha and K. Schulten “Conformational model of the Holliday junction transition deduced from molecular dynamics simulations,” Nucleic Acids Research 32, 6683-6695 (2004).
22. I. Rasnik, S.A. McKinney and T. Ha, “Surfaces and orientations: much to fret about?” Accounts of Chemical Research 38, 542-548 (2005).
23. J. Liu, A. C. Declais, S. A. McKinney, T. Ha, D. G. Norman and D. M. J. Lilley, “Stereospecific effects determine the structure of a four-way DNA junction,” Chemistry & Biology 12, 217-228 (2005).
24. S.A. McKinney, A. Freeman, D. M. J. Lilley and T. Ha, “Observing spontaneous branch migration of Holliday junctions one step at a time,” Proc. Natl. Acad. Sci. USA 102, 5715-5720 (2005).
25. H. Balci, T. Ha, H.L. Sweeney, and P. R. Selvin, “Interhead distance measurements in myosin VI via SHRImP support a simplified hand-over-hand model,” Biophysical J. 89, 413-417 (2005).
26. J. B. Robbins, M. C. McKinney, C. E. Guzman, B. Srinatana, S. Fits-Gibbon, T. Ha and I. K. O. Cann, “The Euryarchaeota: nature's medium for engineering of single-stranded DNA binding proteins,” J. Biol. Chem. 280, 15325-15339 (2005).
27. S. Hohng and T. Ha, “Single-molecule quantum dot FRET,” Chem. Phys. Chem. 6, 956-960 (2005).
28. S. Myong, I. Rasnik, C. Joo, T. M. Lohman and T. Ha, “Repetitive shuttling of a motor protein on DNA,” Nature 437, 1321-1325 (2005).
29. J. Y. Lee, B. Okumus, D.S. Kim and T. Ha, “Extreme conformational diversity of human telomeric DNA,” Proc. Natl. Acad. Sci. USA 102, 18938-18943 (2005).
30. E. Toprak, J. Enderlein, S. Syed, S.A. McKinney, R.G. Petschek, T. Ha, Y. E. Goldman, and P. R. Selvin, “Defocused Orientation and Position Imaging (DOPI) of Myosin V,” Proc. Natl. Acad. Sci. USA 103, 6495-6499 (2006).
31. S. Myong, B.C. Stevens and T. Ha, “Bridging conformational dynamics and function using single-molecule spectroscopy,” Structure 14, 1-11 (2006).
32. C. Buranachai, S.A. McKinney, and T. Ha, “Single molecule nanometronome,” Nano Letters 6, 496-500 (2006).
33. C. Joo, S.A. McKinney, M. Nakamura, I. Rasnik, S. Myong and T. Ha, “Real time observation of RecA filament dynamics with single monomer resolution,” Cell 126, 515-528 (2006).
34. Y. Lin, C. E. Guzman, M. C. McKinney, S. K. Nair, T. Ha, and I. K. O. Cann, “Methanosarcina acetivorans flap endonuclease 1 activity is inhibited by a cognate single-stranded DNA-binding protein,” J. Bacteriology 188(17), 6153-67 (2006).
35. S.A. McKinney, C. Joo and T. Ha, “Analysis of single molecule FRET trajectories using hidden Markov modeling,” Biophysical J. 91, 1941-1951 (2006).
36. J. Yu, T. Ha and K. Schulten, “Structure-based model of the stepping motor of PcrA helicase,” Biophys. J. 91(6), 2097-2114 (2006).
37. I. Rasnik, S. Myong and T. Ha, “Unraveling helicase mechanism one molecule at a time,” Nucleic Acids Research 34, 4225-4231 (2006).
38. I. Rasnik, S. A. McKinney and T. Ha, “Nonblinking and long-lasting single molecule fluorescence imaging,” Nature Methods 3, 891-893 (2006).
39. T. Y. Yoon, B. Okumus, F. Zhang, Y. K. Shin and T. Ha, “Multiple intermediates in SNARE-induced membrane fusion,” Proc. Natl. Acad. Sci. USA 103, 19731-19736 (2006).
40. V. Arluison, S. Hohng, R. Roy, O. Pellegrini, P. Regnier, T. Ha, “Spectroscopic observation of RNA chaperone activities of Hfq in post-transcriptional regulation by a small non-coding RNA,” Nucleic Acids Research 35 (3), 999-1006 (2007).
41. T. J. Wilson, M. Nahas, L. Araki, S. Harusawa, T. Ha, D. M. Lilly, “RNA folding and the origins of catalytic activity in the hairpin ribozyme,” Blood Cells Mol Dis. 38(1), 8-14 (2007).
42. P. V. Cornish and T. Ha, “A survey of single molecule techniques in chemical biology,” ACS Chemical Biology 2(1), 53-61 (2007).
43. R. Roy, A. Kozlov, T. M. Lohman and T. Ha, “Dynamic structural rearrangements between DNA binding modes of E. coli SSB protein,” J. Mol. Biol. 369, 1244–1257 (2007).
44. P. S. Shirude, B. Okumus, L. Ying, T. Ha and S. Balasubramanian, “Single Molecule Conformational Analysis of G-Quadruplex Formation in the Promoter DNA Duplex of the Proto-Oncogene C-kit,” JACS 129, 7484-7485 (2007).
45. T. Ha, “Need for speed: Mechanical regulation of a replicative helicase,” Cell 129, 1249-1250 (2007).
46. S. Myong, M. M. Bruno, A. M. Pyle and T. Ha, “Spring-loaded mechanism of DNA unwinding by HCV NS3 helicase,” Science 317, 513-516 (2007).
47. I. Cisse, B. Okumus, C. Joo and T. Ha, “Fueling DNA-protein interactions inside porous nanocontainers,” PNAS 104, 12646-12650 (2007).
48. J. Yu, T. Ha and K. Schulten, “How Directional Translocation is Regulated in a DNA Helicase Motor,” Biophys. J. Published ahead of print on August 17, 2007 as doi:10.1529/biophysj.107.109546 (2007).
49. S. Hohng, R. Zhou, M. K. Nahas, J. Yu, K. Schulten, D. M. J. Lilley and T. Ha, “Fluorescence-force spectroscopy maps two-dimensional reaction landscape of the Holliday junction,” Science 318, 279-283 (2007).
50. E. Rothenberg, M. A. Trakselis, S. D. Bell and T. Ha, “MCM fork substrate specificity involves dynamic interaction with the 5’ tail,” J. Biol. Chem. 282, 34229-34234 (2007).
51. H. Kim, I. Rasnik, J. Liu, T. Ha and Y. Lu “Dissecting metal ion dependent folding and catalysis of single DNAzyme,” Nature Chemical Biology 3, 763-768 (2007).
52. P. R. Selvin and T. Ha, editors, Single Molecule Techniques: A Laboratory Manual, Cold Spring Harbor Laboratory Press, 507 pp., ISBN 978-087969775-4 (2008).

updated 11/28/2007