Publications

• "A Simplified Model for Lysogenic Regulation Through DNA Looping," L. M. Anderson and H. Yang, to appear in Proceedings of IEEE Engineering in Medicine and Biology Society (2008).

• "Observation of Spectral Anisotropy of Gold Nanoparticles," H. Cang, D. Montiel, C. S. Xu, and H. Yang, J. Chem. Phys., in press (2008).

• "Observation of Correlated Emission Intensity and Polarization Fluctuations in Single CdSe/ZnS Quantum Dots," D. Montiel and H. Yang, J. Phys. Chem. A, in press (2008).

• "A General Statistical Test for Correlations in a Finite-Length Time Series," J. A. Hanson and H. Yang, J. Chem. Phys., 128, 214101 (2008).

• "Model-Free Statistical Reduction of Single-Molecule Time Series," H. Yang, in Theory, Modeling and Evaluation of Single-Molecule Measurements edited by E. Barkai, F. L. H. Brown, M. Orrit, and H. Yang, World Scientific Publishing, in press (2008).

• "Progress in Single-Molecule Tracking Spectroscopy," H. Cang, C. S. Xu, and H. Yang, Chem. Phys. Lett. (FRONTIERS review article), 457, 285-291 (2008). (Cover)

  

• "DNA looping can enhance lysogenic CI transcription in phage lambda," L. M. Anderson and H. Yang, Proc. Natl. Acad. Sci. U.S.A., 105, 5827-5832 (2008).

• "Multiscale Complex Network of Protein Conformational Fluctuations in Single-Molecule Time Series," C. B. Li, H. Yang, and T. Komatsuzaki, Proc. Natl. Acad. Sci. U.S.A., 105, 536-541 (2008).

• "Joint Statistical Analysis of Multi-Channel Time Series from Single Quantum Dot-(Cy5)_n Constructs," C. S. Xu, H. Kim, C. C. Hayden, and H. Yang, J. Phys. Chem. B, 112, 5917-5923 (2008).

• "Illuminating the Mechanistic Roles of Enzyme Conformational Dynamics," J. A. Hanson, K. Duderstadt, L. P. Watkins, S. Bhattacharyya, J. Brokaw, J.-W. Chu, and H. Yang, Proc. Natl. Acad. Sci. U.S.A., 104, 18055-18060 (2007).

• "Guiding a Confocal Microscope by Single Fluorescent Nanoparticles," H. Cang, C. S. Xu, D. Montiel, and H. Yang, Opt. Lett., 32, 2729-2731 (2007). This work was highlighted in the October issue of Nature Photonics, 1, 561 (2007).

• "Single Quantum Dots as Local Temperature Markers," S. Li, K. Zhang, J.-M. Yang, L. Lin, and H. Yang, Nano Lett., 7, 3102-3105 (2007). This work was highlighted in Technology Research News, and also in the November issue of Nanophotonics (2007).

• "Multi-parameter Fluorescence Spectroscopy of Single Quantum Dot-Dye FRET Hybrids," C. S. Xu, H. Kim, H. Yang, and C. C. Hayden, J. Am. Chem. Soc., 129, 11008-11009 (2007). This work was highlighted in the December issue of Biophotonics, 14, 41 (2007).

• "DNA Transformation via Local Heat Shock," S. Li, L. M. Anderson, J.-M. Yang, L. Lin, and H. Yang, Appl. Phys. Lett., 91, 013902 (2007). This work was selected by the Virtual Journal of Biological Physics Research, 14, Jul. 15 (2007), appearing in the DNA CONFORMATIONAL DYNAMICS section.

• "Single-Particle Light Scattering: Imaging and Dynamical Fluctuations in the Polarization and Spectral Response," H. Yang, J. Phys. Chem. A, 111, 4987-4997 (2007).

• "Optically Active Sum Frequency Generation Microscopy for Cellular Imaging," K. Zhang, N. Ji, Y. R. Shen, and H. Yang, Ultrafast Phenomena XV, Eds. P. Corkum, D. Jonas, D. Miller, A. M. Weiner, (Springer-Verlag, Berlin Heidelberg, 2007) p. 825.

• "Rapid and Quantitative Sizing of Nanoparticles Using Three-Dimensional Single-Particle Tracking," C. S. Xu, H. Cang, D. Montiel, and H. Yang, J. Phys. Chem. C, 111, 32-35 (2007).

• "Quantitative Characterization of Changes in Dynamical Behavior for Single-Particle Tracking Studies," D. Montiel, H. Cang, and H. Yang, J. Phys. Chem. B, 110, 19763-19770 (2006).

• "Confocal Three Dimensional Tracking of A Single Nanoparticle with Concurrent Spectroscopic Readouts," H. Cang, C. M. Wong, C. S. Xu, A. H. Rizvi, and H. Yang, Appl. Phys. Lett., 88, 223901 (2006). This work was selected by the Virtual Journal of Nanoscale Science and Technology, 13, Jun. 12 (2006), appearing in the IMAGING SCIENCE AND TECHNOLOGY section. See also the news brief, Analytical Currents, in Analytical Chemistry, Anal. Chem., 78, 5238 (2006).

• "Continuous Distribution of Emission States from Single CdSe/ZnS Quantum Dots," K. Zhang, H. Chang, A. Fu, A.P. Alivisatos, and H. Yang, Nano Lett., 6, 843-847 (2006).

• "Quantitative Single-Molecule Conformational Distributions: A Case Study with Poly-(L-proline)," L. P. Watkins, H. Chang, and H. Yang, J. Phys. Chem. A, 110, 5191-5203 (2006).

• "Three-Dimensional Chiral Imaging by Sum-Frequency Generation," N. Ji, K. Zhang, H. Yang, and Y. R. Shen, J. Am. Chem. Soc., 128, 3482-3483 (2006).

• "Photon-by-Photon Determination of Emission Bursts from Diffusing Single Chromophores," K. Zhang and H. Yang, J. Phys. Chem. B, 109, 21930-21937 (2005).

• "Detection of Intensity Change Points in Time-Resolved Single Molecule Measurements," L. P. Watkins and H. Yang, J. Phys. Chem. B, 109, 617-628 (2005). [software]

• "Discrete Nanostructures of Quantum Dots/AU with DNA," A. Fu, C. M. Micheel, J. Cha, H. Chang, H. Yang, and A. P. Alivisatos, J. Am. Chem. Soc., 126 (35), 10832-10833 (2004).

• "Information Bounds and Optimal Analysis of Dynamic Single Molecule Measurements," L. P. Watkins and H. Yang, Biophys. J., 86, 4015-4029 (2004). [software]

• "Photon-Timing Detector Modules for Single-Molecule Spectroscopy with 60-ps Resolution," I. Rech, M. Ghioni, H. Yang, X.S. Xie, and S. Cova, IEEE Journal of Selected Topics in Quantum Electronics, 10, 788-795 (2004).

• "Protein Conformational Dynamics Probed by Single-Molecule Electron Transfer ," H. Yang, G. Luo, P. Karnchanaphanurach, T.-M. Louie, I. Rech, S. Cova, L. Xun, and X. S. Xie, Science, 302, 262-266 (2003). Perspective by M. Orrit, "The Motions of an Enzyme Soloist," Science, 302, 239-240 (2003). In the News: "Reactions reveal enzyme motions (SCIENCE & TECHNOLOGY CONCENTRATES)," Chemical & Engineering News, p. 56, October 13, (2003). "Measuring a molecule's contortions," Biophotonics, p. 53, December (2003).

• "FAD is a Preferred Substrate and an Inhibitor of Escherichia coli General NAD(P)H:flavin Oxidoreductase," T.-M. Louie, H. Yang, P. Karnchanaphanurach, X. S. Xie, and L. Xun, J. Biol. Chem., 277, 39450-39455(2002).

• "Probing Single Molecule Dynamics Photon by Photon," H. Yang and X. S. Xie, J. Chem. Phys., 117, 10965-10979 (2002).

• "Statistical Approaches for Probing Single Molecule Dynamics Photon by Photon," H. Yang and X. S. Xie, Chem. Phys., 284 423-437 (2002).

• "Ultrafast UV Pump / IR Probe Studies of C-H Activation in Linear, Cyclic and Aryl Hydrocarbons," M. C. Asplund, P. T. Snee, J. S. Yeston, M. J. Wilkens, C. K. Payne, H. Yang, K. T. Kotz, H. Frei, R. G. Bergman, and C. B. Harris, J. Am. Chem. Soc., 124, 10605-10612 (2002).

• "Intramolecular Rearrangements on Ultrafast Timescales: Femtosecond Infrared Studies of Ring Slip in (η¹-C₅Cl₅)Mn(CO)₅" C. K. Payne, P. T. Snee, H. Yang, K. T. Kotz, L. L. Schafer, T. D. Tilley, and C. B. Harris, J. Am. Chem. Soc., 123, 7425-7426 (2001).

• "Femtosecond Infrared Studies of Solvation and Solvent Caging," H. Yang, P. T. Snee, K. T. Kotz, C. K. Payne, and C. B. Harris, J. Am. Chem. Soc., 123, 4204-4210 (2001).

• "Triplet Organometallic Reactivity Under Ambient Conditions: An Ultrafast UV Pump / IR Probe Study," P. T. Snee, C. K. Payne, K. T. Kotz, H. Yang and C. B. Harris, J. Am. Chem. Soc., 123, 2255-2264 (2001).

• "Probing Bond Activation Reactions with Femtosecond Infrared," H. Yang and C. B. Harris, in Ultrafast Infrared and Raman Spectroscopy; M. D. Fayer Ed. (Marcel Dekker, New York, 2001) p. 81.

• "Ultrafast Infrared Studies of Ligand Rearrangement at Coordinatively Unsaturated Transition Metal Centers," K. T. Kotz, H. Yang, P. T. Snee, C. K. Payne, and C. B. Harris, in Ultrafast Phenomena XII, Eds. T. Elsaesser, S. Mukamel, M. M. Murnane, and N. F. Scherer (Springer-Verlag, Berlin Heidelberg, 2000) p. 636.

• "Femtosecond Infrared Studies of Ligand Rearrangement Reactions: Silyl Hydride Products from Group 6 Carbonyls," K. T. Kotz, H. Yang, P. T. Snee, C. K. Payne, and C. B. Harris, J. Organomet. Chem., 596, 183-192 (2000).

• "Femtosecond Infrared Studies of the Mechanism of Silicon-Hydrogen Bond Activation by η⁵-CpV(CO)₄," P. T. Snee, H. Yang, K. T. Kotz, C. K. Payne, and C. B. Harris, J. Phys. Chem. A, 103, 10426-10432 (1999).

• "Femtosecond Infrared Studies of a Prototypical One-Electron Oxidative-Addition Reaction: Chlorine Atom Abstraction by the Re(CO)₅ Radical," H. Yang, P. T. Snee, K. T. Kotz, C. K. Payne, H. Frei, and C. B. Harris. J. Am. Chem. Soc., 121, 9227-9228 (1999).

• "Femtosecond Infrared Studies of Chemical Bond Activation," M. C. Asplund, H. Yang, K. T. Kotz, S. E. Bromberg, M. J. Wilkens, and C. B. Harris, Laser Chem., 19, 253-262 (1999).

• "Ultrafast Infrared Studies of Bond Activation in Organometallic Complexes," H. Yang, K. T. Kotz, M. C. Asplund, M. J. Wilkens, and C. B. Harris, Acc. Chem. Res., 32, 551-560 (1999). (Cover)

• "The Reaction Mechanism of Silicon-Hydrogen Bond Activation Studied Using Femtosecond to Nanosecond IR Spectroscopy and ab initio Methods," H. Yang, M. C. Asplund, K. T. Kotz, M. J. Wilkens, H. Frei, and C. B. Harris, J. Am. Chem. Soc., 120, 10154 (1998). In the News: "Steps in Si-H bond activation revealed (NEWS OF THE WEEK)," Chemical & Engineering News, p. 17, October 12, (1998).

• "The Mechanism of a C-H Bond Activation Reaction in Room Temperature Alkane Solution," S. E. Bromberg, H. Yang, M. Asplund, T. Lian, B. McNamara, K. T. Kotz, J. S. Yeston, M. J. Wilkens, H. Frei, R. G. Bergman, and C. B. Harris, Science, 278, 260 (1997). (Cover) In the News: "Real-world C-H bond activation (NEWS OF THE WEEK)," Chemical & Engineering News, p. 4, October 13, (1997).

  

• "Femtosecond Infrared Studies of Silane Silicon-Hydrogen Bond Activation," H. Yang, K. T. Kotz, M. C. Asplund, and C. B. Harris, J. Am. Chem. Soc., 119, 9564 (1997).

• "Femtosecond Infrared Studies of the Dissociation and Dynamics of Transition Metal Carbonyls in Solution," T. Lian, S. E. Bromberg, M. C. Asplund, H. Yang, and C. B. Harris, J. Phys. Chem., 100, 11994, (1996).

• "Femtosecond IR studies of Alkane C-H Bond Activation by Organometallic Compounds: Direct Observation of Reactive Intermediates in Room Temperature Solutions," T. Lian, S. E. Bromberg, H. Yang, G. Proulx, R. G. Bergman, and C. B. Harris, J. Am. Chem. Soc., 118, 3769 (1996).

• "Femtosecond IR Studies of Alkane C-H Bond Activation by Organometallic Compounds," T. Lian, S. E. Bromberg, H. Yang, M. Asplund, R. G. Bergman, and C. B. Harris, in Ultrafast Phenomena X, Eds. P. F. Barbara, J. G. Fujimoto, W. H. Knox, and W. Zinth (Springer-Verlag, Berlin Heidelberg, 1996) p.237.

• "Femtosecond IR Studies of Solvation by Probing the Solvent," T. Lian, H. Yang, M. Asplund, S. E. Bromberg, and C. B. Harris, in Ultrafast Phenomena X, Eds. P. F. Barbara, J. G. Fujimoto, W. H. Knox, and W. Zinth (Springer-Verlag, Berlin Heidelberg, 1996) p.300.

• "Molecular Complex between Lithium and Formaldehyde: An ab Initio Molecular Orbital Study," H. Yang, Y.-H. Liau, and T.-M. Su, J. Phys. Chem., 99, 177, (1995).

• "Laser Induced Lasing in CS₂ Vapor," H.-T. Liou, H. Yang, and P. Dan, Appl. Phys. B, 54, 221 (1992).

• "The predissociation of CS₂ at 210 nm and the spectra of photofragment CS," H.-T. Liou, P. Dan, T. Y. Hsu, H. Yang, and H.-M. Lin, Chem. Phys. Lett., 192, 560 (1992).

• "Successive single rotational level radiative decay lifetime measurements of CS₂: evidence of state mixing caused by rotational coupling," H.-T. Liou, H. Yang, N. C. Wang, and R. W. Joy, Chem. Phys. Lett., 178, 80 (1991).

• "Stimulated emission pumping to the rotationally resolved state v = (0, 22, 0) of the ground electronic state of CS₂ by three-level polarization spectroscopy," H.-T. Liou, P. Dan, H. Yang, and J.-Y. Yuh, Chem. Phys. Lett., 176, 109 (1991).

• "Laser Induced Lasing in CS₂ Vapor," H.-T. Liou, P. Dan, H. Yang, R. W. Joy, N. C. Wang, and J. Y. Yuh: In Laser Spectroscopy IX, Eds. M. S. Feld, J. E. Thomas, and A. Mooradian; Academic Press, New York, 1989, p. 429.