THE HAW YANG LAB

: Chemical Dynamics of Single Proteins
: Real-Time 3D Single-Particle Tracking and 3D Multi-Resolution Imaging
: Physical Materials and Materials Biology
: Artificial Swimmers and Active Matter
: Statistical Machine Learning

"The Ever-Expanding Optics of Single-Molecules and Nanoparticles," Frank Cichos, Tie Xia, Haw Yang, and Peter Zijlstra, J. Chem. Phys., 161, 010401 (2024).
"Polyelectrolyte-Doped Block Copolymer-Stabilized Nanocarriers for Continuous Tunable Surface Charge," Brian K. Wilson, Haw Yang, and Robert K. Prud'homme, ACS Appl. Nano Mater., 7, 11071-11079 (2024).
“Sub-Domain Dynamics Enable Chemical Chain Reactions in Nonribosomal Peptide Synthetases,” Xun Sun, Jonas Alfermann, Hao Li, Maxwell B. Watkins, Yi-Tsao Chen, Thomas E. Morrell, Florian Mayerthaler, Chia-Ying Wang, Tamiki Komatsuzaki, Jhih-Wei Chu, Nozomi Ando, Henning D. Mootz, and Haw Yang, Nat. Chem., 16, 259-268 (2024).

See Xun's Behind-the-Paper Blog.

“Trajectory Statistical Learning of the Potential Mean of Force and Diffusion Coefficient from Molecular Dynamics Simulations,” Yi-Tsao Chen, Haw Yang, and Jhih-Wei Chu, J. Phys. Chem. B, 128, 56-66 (2024).
“Mechanical Codes of Chemical-Scale Specificity in DNA Motifs,” Yi-Tsao Chen, Haw Yang, and Jhih-Wei Chu, Chem. Sci., 14, 10155-10166 (2023).
“An Ingestible Pill with CMOS Fluorescence Sensor Array, Bi-directional Wireless Interface and Packaged Optics for in-vivo Bio-molecular Sensing,” Chengjie Zhu, Yuhan Wen, Tao Liu, Haw Yang and Kaushik Sengupta, IEEE Trans. Biomed. Circuits Syst., 17, 257-272 (2023).
"The Trajectory Patterns of Single HIV-1 Virus-like Particle in Live CD4 Cells: A Real Time Three-dimensional Multi-resolution Microscopy Study Using Encapsulated Nonblinking Giant Quantum Dot," Wei-You Li, Shuhui Yin, Szu-Wei Huang, Ming-Hui Yang, Shang-Rung Wu, Kevin Welsher, Haw Yang, and Yi-Ming Arthur Chen, J. Microbiol. Immunol. Infect., 56, 257-266 (2023).
“Parabolic Potential Surfaces Localize Charge Carriers in Non-blinking Long-lifetime ‘Giant’ Quantum Dots,” Marcell Pálmai, Joseph S. Beckwith, Nyssa T. Emerson, Tian Zhao, Eun Byoel Kim, Shuhui Yin, Prakash Parajuli, Kyle Tomczak, Ming Tien, Robert F. Klie, Haw Yang, and Preston T. Snee, Nano Lett., 22, 9470-9476 (2022).
"A Packaged Multiplexed Fluorescent Biomolecular Sensor Array and Ultralow-Power Wireless Interface in CMOS for Ingestible Electronic Applications," Chengjie Zhu, Lingyu Hong, Haw Yang, and Kaushik Sengupta, IEEE Sens. J., 22, 24060-24074 (2022).
"Multicolor multifocal 3D microscopy using in-situ optimization of a spatial light modulator," M. Junaid Amin, Tian Zhao, Haw Yang, and Joshua W. Shaevitz, Sci. Rep., 12, 16343 (2022).
"Sorting Nanoparticles by Valency with DNA Barcoding," Nyssa T. Emerson and Haw Yang, J. Am. Chem. Soc., 144, 12915-12923 (2022).
"Amplifying Intermolecular Events by Streptavidin-Induced Proximity," Hao Li, Tao Liu, and Haw Yang, J. Am. Chem. Soc., 144, 11377-11385 (2022).
"Structure-Mechanics Statistical Learning Uncovers Mechanical Relay in Proteins," Nixon Raj, Nixon, Timothy Click, Haw Yang, and Jhih-Wei Chu, Chem. Sci., 13, 3688-3696 (2022).
"Sub-ms Translational and Orientational Dynamics of A Freely Moving Single Nanoprobe," Joseph S. Beckwith and Haw Yang, J. Phys. Chem. B, 125, 13436-13443 (2021). [W.E. Moerner Festschrift]
"Information Bounds in Determining the 3D Orientation of a Single Emitter or Scatterer using Point-detector-based Division-of-amplitude Polarimetry," Joseph S. Beckwith and Haw Yang, J. Chem. Phys., 115, 144110 (2021).
"Mechanical Couplings of Protein Backbone and Side Chains Exhibit Scale-free Network Properties and Specific Hotspots for Function," Nixon Raj, Timothy Click, Haw Yang, and Jhih-Wei Chu, Comput. Struct. Biotechnol. J., 19, 5309-5320 (2021).
"Leveraging lifetime information to perform real-time 3D single-particle tracking in noisy environments," Tian Zhao, Joseph S. Beckwith, M. Junaid Amin, Marcell Pálmai, Preston T. Snee, Ming Tien, and Haw Yang, J. Chem. Phys., 155, 164201 (2021). (Cover Story)

This work has been noted by the following media:

• In AIP Scilight, "Microscope design promises breakthrough in 3D single-particle tracking," by Ben Ikenson.

• In Princeton Chemistry News, "YANG ADVANCES SINGLE-MOLECULE TRACKING WITH NOVEL IMAGING METHOD," by Wendy Plump.

• In U.S. Department of Energy University and Stakeholder News, "Yang Advances Single-Molecule Tracking with Novel Imaging Method."

• In Editors' Choice Article 2021, under the "Advanced Experimental Techniques" category.

"Localization precision in chromatic multifocal imaging," M. Junaid Amin, Sabine Petry, Joshua W. Shaevitz, Haw Yang, J. Opt. Soc. Am. B, 38, 2792-2798 (2021); see also arXiv:2008.10488 [physics.optics] (2020).
"Reproducibly measuring plasmon-enhanced fluorescence in bulk solution across a 20-fold range of optical densities," Nyssa T. Emerson and Haw Yang, Anal. Chem., 93, 8045-8053 (2021).
"Intermediary conformations linked to the directionality of the aminoacylation pathway of nonribosomal peptide synthetases," Florian Mayerthaler, Anna-Lena Feldberg, Jonas Alfermann, Xun Sun, Wieland Steinchen, Haw Yang, Henning D.Mootz, RSC Chem. Biol., 2, 843-854 (2021).
"Intensity uniformity optimization in spatial light modulator-based multifocal microscope," M. Junaid Amin, Sabine Petry, Haw Yang, Joshua W. Shaevitz, Proc. SPIE, Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXVIII, 11649OP (2021).
"Three-dimensional super line-localization in low signal-to-noise microscope images via prior-apprised unsupervised learning (PAUL)," Shuhui Yin, M. Junaid Amin, Nyssa T. Emerson, and Haw Yang, Proc. SPIE, Applications of Digital Image Processing XLIII, 11510, 115101L (2020).
"A Packaged Ingestible Bio-pill with 15-pixel Multiplexed Fluorescence Nucleic-acid Sensor and Bi-directional Wireless Interface for In-vivo Bio-molecular Sensing," Chengjie Zhu, Yuhan Wen, Tao Liu, Haw Yang, and Kaushik Sengupta, IEEE VLSI Sumposium on VLSI Circuits, 1-2 (2020).
"Structure-Mechanics Statistical Learning Unravels the Linkage between Local Rigidity and Global Flexibility in Nucleic Acids," Yi-Tsao Chen, Haw Yang, and Jhih-Wei Chu, Chem. Sci., 11, 4969-4979 (2020).
"Prior-Apprised Unsupervised Learning of Sub-Pixel Curvilinear Features in Low Signal-to-Noise Images," Shuhui Yin, Ming Tien, and Haw Yang, Biophys. J., 118, 2458-2469 (2020).
"Uniform intensity in multifocal microscopy using a spatial light modulator," M. Junaid Amin, Sabine Petry, Haw Yang, and Joshua W. Shaevitz, PLoS ONE, 15, e0230217 (2020).
"Photobleaching Statistics in Single-Molecule On-/Off-Time Distributions," Haw Yang, Hao Li, and Tao Liu, J. Chem. Phys., 151, 174101 (2019).
"Determining the Spheroid Geometry of Individual Metallic Nanoparticles by Two-Dimensional Single-Particle Dynamic Light Scattering," Luis F. Guerra, Tom W. Muir, and Haw Yang, J. Phys. Chem. C, 123, 18565-18572 (2019).
"Single-particle Dynamic Light Scattering: Shapes of Individual Nanoparticles," Luis F. Guerra, Tom W. Muir, and Haw Yang, Nano Lett., 19, 5530-5536 (2019).
"Statistical Learning of Discrete States in Time Series," Hao Li and Haw Yang, J. Phys. Chem. B, 123, 689-701 (2019).
"Compound Molecular Logic in Accessing the Active Site of M. Tuberculosis Protein Tyrosine Phosphatase B," Thomas E. Morrell, Ilona Rafalska-Metcalf, Haw Yang and Jhih-Wei Chu, J. Am. Chem. Soc., 140, 14747-14752 (2018).
"Nano-plasmonics and electronics co-integration in CMOS enabling a pill-sized multiplexed fluorescence microarray system," Lingyu Hong, Hao Li, Haw Yang, and Kaushik Sengupta, Biomed. Opt. Express, 9, 5735-5758 (2018).
"Active Particles Bound by Information Flows," Utsab Khadka, Viktor Holubec, Haw Yang, and Frank Cichos, Nat. Commun., 9, 3864 (2018).
"Integrated Copper-based Sub-wavelength Angle-insensitive Nano-plasmonic Filters for Ultra-miniaturized Fluorescence Microarray in a 65-nm Digital CMOS Process," Lingyu Hong, Hao Li, Haw Yang, and Kaushik Sengupta, ACS Photonics, 5, 4312-4322 (2018).
"Theory for Controlling Individual Self-Propelled Micro-swimmers by Photon Nudging II: Confinement," Markus Selmke, Utsab Khadka, Andreas P. Bregulla, Frank Cichos, and Haw Yang, Phys. Chem. Chem. Phys., 20, 10521-10532 (2018).
"Theory for Controlling Individual Self-Propelled Micro-swimmers by Photon Nudging I: Directed Transport," Markus Selmke, Utsab Khadka, Andreas P. Bregulla, Frank Cichos, and Haw Yang, Phys. Chem. Chem. Phys., 20, 10502-10520 (2018).
"A Versatile Optical Microscope for Time-Dependent Single-Molecule and Single-Particle Spectroscopy," Hao Li and Haw Yang, J. Chem. Phys., 148, 123316 (2018).
"Detection of Velocity and Diffusion Coefficient Change Points in Single-Particle Trajectories," Shuhui Yin, Nancy Song, and Haw Yang, Biophys. J., 115, 217-229 (2018). [corrigendum-20211013]
"Parallelization of Change Point Detection," Nancy Song and Haw Yang, J. Phys. Chem. A, 121, 5100-5109 (2017).
"FRET monitoring of a nonribosomal peptide synthetase," Jonas Alfermann, Xun Sun, Florian Mayerthaler, Thomas E. Morrell, Eva Dehling, Gerrit Volkmann, Tamiki Komatsuzaki, Haw Yang, and Henning D. Mootz, Nat. Chem. Biol., 13, 1009-1015 (2017).
"Fully Integrated Fluorescence Biosensors on-chip Employing Multi-functional Nanoplasmonic Optical Structures in CMOS," Lingyu Hong, Hao Li, Haw Yang, and Kaushik Sengupta, IEEE Journal of Solid Circuits, 52, 2388-2406 (2017).
"Identifying the Structural and Kinetic Elements in Protein Large-Amplitude Conformational Motions," Jhih-Wei Chu and Haw Yang, Int. Rev. Phys. Chem., 36, 185-227 (2017). (Cover Story)
"Extraction of protein conformational modes from distance distributions using structurally imputed Bayesian data augmentation," Xun Sun, Thomas E. Morrell, and Haw Yang, J. Phys. Chem. B, 120, 10469-10482 (2016).
"Plasmonics, Tracking and Manipulating, and Living Cells: General Discussion," Thorben Cordes, William Moerner, Michel Orrit, Sergey Sekatskii, Sanli Faez, Paola Borri, Himangshu Prabal Goswami, Alex Clark, Patrick El-Khoury, Sandra Mayr, Jacek Mika, Guowei Lyu, Daniel Cross, Francisco Balzarotti, Wolfgang Langbein, Vahid Sandoghdar, Jens Michaelis, Arindam Chowdhury, Alfred J. Meixner, Niek van Hulst, Brahim Lounis, Fernando Stefani, Frank Cichos, Maxime Dahan, Lukas Novotny, Mark Leake and Haw Yang, Faraday Discuss., 184, 451-473 (2015).
"Imaging the behavior of molecules in biological systems: Breaking the 3D speed barrier with 3D Multi-resolution Microscopy," Kevin Welsher and Haw Yang, Faraday Discuss., 184, 359-379 (2015). (Cover Story)
"A Fully integrated CMOS fluorescence biosensor with on-chip nanophotonic filter," Lingyu Hong, Simon McManus, Haw Yang, and Kaushik Sengupta, 2015 Symposia on VLSI Technology and Circuits, Kyoto, Japan, June 15-19, 2015.
"Discovery of protein- and DNA-imperceptible nanoparticle hard coating using gel-based reaction tuning," K. Welsher, S. A. McManus, C.-H. Hsia, S. Yin, H. Yang, J. Am. Chem. Soc., 137, 580-583 (2015) (Communication).
"Kinetics profiling of gramicidin S synthetase A, a member of nonribosomal peptide synthetases," X. Sun, H. Li, J. Alfermann, H. Mootz, H. Yang, Biochemistry, 53, 7983-7989 (2014).
"The 'plug-and-go' strategy to manipulate streptavidin valencies," X. Sun, D. Montiel, H. Li, and H. Yang, Bioconjugate Chem., 25, 1375-1380 (2014).
"Stochastic Localization of Micro-Swimmers by Photon Nudging," A. Bregulla, H. Yang, F. Cichos, ACS Nano, 8, 6542-6550 (2014).
"Analysis of Trajectory Entropy for Continuous Stochastic Processes at Equilibrium," K. R. Haas, H. Yang, and J.-W. Chu, J. Phys. Chem. B, 118, 8099-8107 (2014).
"The Trajectory Entropy of Continuous Stochastic Processes at Equilibrium," K. R. Haas, H. Yang, and J.-W. Chu, J. Phys. Chem. Lett., 5, 999-1003 (2014).
"Mechanodelivery of Nanoparticles to the Cytoplasm of Living Cells," N. T. Emerson, C.-H. Hsia, I. U. Rafalska-Metcalf, and H. Yang, Nanoscale, 6, 4538-4543 (2014).
"Multi-resolution 3D Visualisation of the Early Stages of Cellular Uptake of Peptide-coated Nanoparticles," K. Welsher and H. Yang, Nat. Nanotechnol., 9, 198-203 (2014). This work has been noted by the following media: • In Discovery: Research at Princeton, "Captured on video: Virus-sized particle trying to enter cell," by Catherine Zandonella. • In Nanowerk, "Now in 3-d: video of virus-sized particle trying to enter cell (w/video)." • In Scicasts, "Now in 3-D: Video of Virus-Sized Particle Trying to Enter Cell." • In PÚBLICO, "Viu-se pela primeira vez um vírus artificial a tentar entrar numa célula." • In CNET, "Watch a virus-like particle try to enter a cell -- in 3D," by Elizabeth Armstrong Moore. • In Science Daily, "Now in 3-D: Video of virus-sized particle trying to enter cell." • In Princeton Journal Watch (with video) and EurekAlert!, "Now in 3D: Video of virus-sized particle trying to enter cell," by Catherine Zandonella. • JWJ of Atoms Up reported this work in "The Invisible, Now Visible: New Technology Can Track Virus Sized Particles."
"Fisher Information Metric for the Langevin Equation and Least Informative Models of Continuous Stochastic Dynamics," K. R. Haas, H. Yang, and J.-W. Chu, J. Chem. Phys., 139, 121931 (2013).
"Expectation-Maximization of the Potential of Mean Force and Diffusion Coefficient in Langevin Dynamics from Single-Molecule FRET Data Photon by Photon," K. R. Haas, H. Yang, and J.-W. Chu, J. Phys. Chem. B, 117, 15591-15605 (2013).
"Numerical Construction of Estimators for Single-Molecule Fluorescence Measurements," S. Kawai, D. Cooper, C. Landes, H. D. Mootz, H. Yang, and T. Komatsuzaki, in J. Phys. Chem. B, 117, 8061-8074 (2013).
"Confocal Single-Molecule FRET for Protein Conformational Dynamics," Y.-W. Tan, J. A. Hanson, J.-W. Chu, and H. Yang, in Protein Dynamics: Methods and Protocols in the Methods in Molecular Biology series, vol. 1084, Ed. Dennis R. Livesay, September 30 (2013).
"Harnessing Thermal Fluctuations for Purposeful Activities: The Manipulation of Single Micro-swimmers by Adaptive Photon Nudging," B. Qian, D. Montiel, A. Bregulla, F. Cichos, and H. Yang, Chem. Sci. 4, 1420-1429 (2013). (Cover Story) This work has been noted by the following news media: • Chemistry World, "Manipulating microswimmers."
"Ligand Synthesis and Passivation for Silver and Large Gold Nanoparticles for Single-Particle-Based Sensing and Spectroscopy," D. Montiel, E. V. Yates, L. Sun, M. M. Sampias, J. Malona, E. J. Sorensen, and H. Yang, in Nanomaterial Interfaces in Biology: Methods and Protocols in the Methods in Molecular Biology series, vol. 1025, Eds. Kimberly Hamad-Schifferli and Paolo Bergese, August 31 (2013).
"Quantitative in vitro Biochemistry, one molecule at a time," J. A. Hanson and H. Yang, in Quantitative Biology: From Molecular to Cellular Systems, Edited by Michael E. Wall, Taylor and Francis Group, August (2012).
"Structural Distributions from Single-Molecule Measurements as a Tool for Molecular Mechanics," J. A. Hanson, J. Brokaw, C. C. Hayden, J.-W. Chu, and H. Yang, Chem. Phys., 396, 61-67 (2012).
"Model-Free Analysis of Time-Dependent Single-Molecule Spectroscopy," K. Welsher and H. Yang, Proceedings of the 9^th IEEE International Symposium on Biomedical Imaging, pp. 921-923, Barcelona, Spain, May 2012.
"An Accessible Approach to Preparing Water-Soluble Mn²⁺-doped (CdSSe)ZnS (Core)Shell Nanocrystals for Ratiometric Temperature Sensing," C.-H. Hsia, A. Wuttig, and H. Yang, ACS Nano, 5, 9511-9522 (2011).
"Quantum Dot Nano Thermometers Reveal Heterogeneous Local Thermogenesis in Living Cells," J.-M. Yang, H. Yang, and L. Lin, ACS Nano, 5, 5067-5071 (2011). This work has been noted by the following media: • in the 242^nd ACS National Meeting at Denver. See ACS press release, "Nano-thermometers show first temperature response differences within living cells." • The Scientist magazine, "Next Generation: Cellular Nanothermometer." • TempSensorNews, "Temps for Individual Cells." • Laser Focus World, "Quantum dots take the temperatures of points within a single living cell." • PRLog, "Nano-thermometers and Quantum Mechanics."
"Seeing the Forest for the Trees: Fluorescence Studies of Single Enzymes in the Context of Ensemble Experiments," Y.-W. Tan and H. Yang, Phys. Chem. Chem. Phys., 13, 1709 (2011).
"Change-Point Localization and Wavelet Spectral Analysis of Single-Molecule Time Series," H. Yang, Adv. Chem. Phys., 146, 219 (2011).
"Engagement of Arginine Finger to ATP Triggers Large Conformational Changes in NtrC1 AAA+ ATPase For Remodeling Bacterial RNA Polymerase," B. Chen, T. A. Sysoeva, S. Chowdhury, M. Rusu, S. Birmanns, J. A. Hanson, H. Yang, L. Guo, B. T. Nixon, Structure, 18, 1420 (2010). (Cover) Commentary by M. Buck and T. R. Hoover, Structure, 18, 1391 (2010).
"Origin Remodeling and Opening in Bacteria Relies on Distinct Assembly States of the DnaA Initiator," K. E. Duderstadt, M. L. Mott, N. J. Crisona, K. Chuang, H. Yang, J. M. Berger, J. Biol. Chem., 285, 28229 (2010).
"Thermogenesis Detection of Single Living Cells via Quantum Dots," J.-M. Yang, H. Yang, and L. Lin, in Proceedings of 23^rd IEEE Micro Electro Mechanical Systems Conference, pp. 963-966, Hong Kong, Jan. 2010.
"Analysis of Large-Amplitude Conformational Transition Dynamics in Proteins at the Single-Molecule Level," H. Yang, in Cell Signaling Reactions: Single-Molecular Kinetic Analysis, Edited by Yasushi Sako and Masahiro Ueda, Springer, November 29 (2010).
"Real-Time Three-Dimensional Single-Particle Tracking Spectroscopy for Complex Systems," D. Montiel and H. Yang, Laser & Photonics Reviews, 3, 374 (2010). (Published on-line: June 2, 2009)
"Dynamic active site protection by the M. tuberculosis protein tyrosine phosphatase PtpB lid domain," E. M. Flynn, J. A. Hanson, T. Alber, and H. Yang, J. Am. Chem. Soc., 132, 4772 (2010).
"Progress in Single-Molecule Spectroscopy in Cells," H. Yang, Curr. Opin. Chem. Biol., 14, 3-9 (2010). (Cover)
"The Orientation Factor in Single-Molecule Förster-Type Resonance Energy Transfer with Examples for Conformational Transitions in Proteins," H. Yang, Israel J. Chem., 49, 313-322 (2009). (Cover)
"A New Quantification of Local Transition Heterogeneity of Multiscale Complex Networks Constructed from Single-Molecule Time Series," C. B. Li, H. Yang, and T. Komatsuzaki, J. Phys. Chem. B, 113, 14732 (2009).
"Real-Time Chemical Imaging of Bacterial Activity in Biofilms Using Open-Channel Microfluidics and Synchrotron FTIR Spectromicroscopy," H.-Y. N. Holman, R. Miles, Z. Hao, E. Wozei, L. M. Anderson, H. Yang, Anal. Chem., 81, 8564 (2009).
"Unraveling the Dynamics Bridging Protein Structure and Function One Molecule at a Time," J. A. Hanson, Y.-W. Tan, and H. Yang, in Single Particle Tracking and Single Molecule Energy Transfer: Applications in the Bio and Nano Sciences, Editd by C. Bräuchle, D. Lamb, and J. Michaelis, Wiley-VCH (2010), published Dec. 18, 2009.
"Bipolar Cellular Morphology of Malignant Melanoma in Unstained Human Melanoma Skin Tissue," K. Zhang, W.-K. Zhang, C.-Y. Yang, and H. Yang, J. Biomed. Opt., 14, 024042 (2009).
"Direct Mg²⁺ binding activates Adenylate Kinase from Escherichia coli," Y.-W. Tan, J. A. Hanson, and H. Yang, J. Biol. Chem., 284, 3306-3313 (2009).
"Quantitative Evaluation of Cross-Correlation between Two Finite-Length Time Series with Applications to Single-Molecule FRET," J. A. Hanson and H. Yang, J. Phys. Chem. B, 112, 13962-13970 (2008).
"Detection and Characterization of Dynamical Heterogeneity in an Event Series Using Wavelet Correlation," H. Yang, J. Chem. Phys., 129, 074701 (2008). [corrigenda-20180911] This work was selected by the Virtual Journal of Biological Physics Research, 16, Aug. 15 (2008), appearing in the SINGLE MOLECULE DYNAMICS section.
"A Simplified Model for Lysogenic Regulation Through DNA Looping," L. M. Anderson and H. Yang, Proceedings of the 30^th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, pp 607–610, Vancouver, Canada, Aug. 20-24, (2008).
"Observation of Spectral Anisotropy of Gold Nanoparticles," H. Cang, D. Montiel, C. S. Xu, and H. Yang, J. Chem. Phys., 129, 044503 (2008). This work was selected by the Virtual Journal of Nanoscale Science & Technology, 18, Aug. 4 (2008), appearing in the OPTICAL PROPERTIES AND QUANTUM OPTICS section.
"Observation of Correlated Emission Intensity and Polarization Fluctuations in Single CdSe/ZnS Quantum Dots," D. Montiel and H. Yang, J. Phys. Chem. A, 112, 9352-9355 (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 and Evaluation of Single-Molecule Signals edited by E. Barkai, F. L. H. Brown, M. Orrit, and H. Yang, World Scientific Publishing, October (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) (Communication). 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). [corrigenda-20181001]
"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.
"MEMS Temperature Characterization by CdSe Quantum Dots ," S. Li, K. Zhang, J.-M. Yang, L. Lin, and H. Yang, The 14^th International Conference on Solid-State Sensors, Actuators and Microsystems, 1369-1372, Lyon, France, June (2007).
"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).
"DNA transformation by local heat shock," S. Li, L. M. Anderson, L. Lin, and H. Yang, Proceedings of the 20^th IEEE Micro Electro Mechanical Systems Conference, 533-536, Kobe, Japan, January (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). [corrigendum-20211013]
"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] [corrigenda]
"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).
"Ultrafast Infrared Studies of the Reaction 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.