Nagwan I. Ali
Frick Laboratory, 128
The Haw Yang Lab works on problems in the general area of Biophysical Dynamics. On the more abstract level, we seek to understand the manner by which local fluctuations in a complex system may contribute to the system’s function. Examples include how proteins exploit thermally driven conformational changes to achieve their functions, how living cells modulate their intra-cellular local temperature to remain viable, how viruses or nanomedicine carriers dynamically interact with a cell to infect the cell or to accomplish cellular delivery, and how one can control the nanoscale interfacial hydrodynamical fluctuations to manipulate micro- and nano-swimmers in three dimensions (3D).
In order to address problems like these, we have successfully developed several original experimental approaches. Because many of the experiments are new, we also develop the required theories concurrently. For example, for single-molecule protein dynamics in molecular biophysics, our photon-by-photon method treats each detected photon as a data point so that the conformational distribution of a protein and the dynamical evolution of its conformational can be quantitatively evaluated with highest possible resolution without any presumed model. For cellular thermobiology, we have been actively advancing nanothermometer-based local temperature metrology that will permit us to measure the temperature of a specific cellular organelle precisely and rapidly.
For nanomedicine, we have developed the 3D multi-resolution microscopy concept, by which the current implementation allows us to make high-definition real-time motion pictures of a virus or nanoparticle with 10-μs time resolution and ~10-nm spatial localization precision in all three dimensions. For the 3D control of micro- and nano-swimmers, we have put forward the “photon nudging” idea, in which the “engine” of a self-propelled swimmer is stochastically turned on and off using a very weak laser light based on the swimmer’s location and orientation. These new experimental approaches have allowed us to look at problems from new perspectives and, in many instances, have enabled interesting new discoveries.
Fellow of the Royal Society of Chemistry (2013)
The Xingda Lecture, Peking University (2012)
Fudan University Key Laboratory Senior Visiting Scholar (2012 – 2013)
Camille Dreyfus Teacher-Scholar Award (2008 – 2013)
Alfred P. Sloan Research Fellow (2006 – 2008)
Hellman Family Faculty Fund Award (2005)
NSF Career Award, National Science Foundation (2004)
Graduate Student Traveling Scholarship of the 44th Annual Conference of the Western Spectroscopy Association (1997)
Shu-Chuang Award (top 5% in a class; also translated as Book Coupon Award), National Taiwan University (4 consecutive years, 1988 – 1991)
Yuan T. Lee Chemistry Scholarship, China Technical Consultants, Inc. (1987 – 1991)
Gifted Student Scholarship in Chemistry, Administration of Education, Taiwan (exempt from the College entrance exam with 4 years of tuition, 1987 – 1991)
Sun, X.; Montiel, D.; Li, H.; Yang, H., "The 'plug-and-go' strategy to manipulate streptavidin valencies." Bioconjugate Chem., 2014, 25, 1375-1380.
Tan, Y.-W.; Hanson, J. A.; Chu, J.-W.; Yang, H., "Confocal Single-Molecule FRET for Protein Conformational Dynamics." In Protein Dynamics: Methods and Protocols, Livesay, D. R., Ed. 2014; Vol. 1084, pp 51-62.
Haas, K. R.; Yang, H.; Chu, J.-W., "Analysis of Trajectory Entropy for Continuous Stochastic Processes at Equilibrium." Journal of Physical Chemistry B 2014, 118 (28), 8099-8107.
Welsher, K.; Yang, H., "Multi-resolution 3D visualization of the early stages of cellular uptake of peptide-coated nanoparticles." Nature Nanotechnology 2014, 9 (3), 198-203.
Sun, X.; Montiel, D.; Li, H.; Yang, H., "“Plug-and-Go” Strategy To Manipulate Streptavidin Valencies." Bioconjugate Chemistry 2014, 25 (8), 1375-1380.
Bregulla, A. P.; Yang, H.; Cichos, F., "Stochastic Localization of Microswimmers by Photon Nudging." Acs Nano 2014, 8 (7), 6542-6550.
Emerson, N. T.; Hsia, C.-H.; Rafalska-Metcalf, I. U.; Yang, H., "Mechanodelivery of nanoparticles to the cytoplasm of living cells." Nanoscale 2014, 6 (9), 4538-4543.
Haas, K. R.; Yang, H.; Chu, J.-W., "Trajectory Entropy of Continuous Stochastic Processes at Equilibrium. "Journal of Physical Chemistry Letters 2014, 5 (6), 999-1003.
Montiel, D.; Yates, E. V.; Sun, L.; Sampias, M. M.; Malona, J.; Sorensen, E. J.; Yang, H., "Ligand Synthesis and Passivation for Silver and Large Gold Nanoparticles for Single-Particle-Based Sensing and Spectroscopy." In Nanomaterial Interfaces in Biology: Methods and Protocols, Bergese, P.; HamadSchifferli, K., Eds. 2013; Vol. 1025, pp 237-250.
Haas, K. R.; Yang, H.; Chu, J.-W., "Fisher information metric for the Langevin equation and least informative models of continuous stochastic dynamics." Journal of Chemical Physics 2013, 139 (12).
Haas, K. R.; Yang, H.; Chu, J.-W., "Expectation-Maximization of the Potential of Mean Force and Diffusion Coefficient in Langevin Dynamics from Single Molecule FRET Data Photon by Photon." Journal of Physical Chemistry B 2013, 117 (49), 15591-15605.
Kawai, S.; Cooper, D.; Landes, C.; Mootz, H. D.; Yang, H.; Komatsuzaki, T., "Numerical Construction of Estimators for Single-Molecule Fluorescence Measurements." Journal of Physical Chemistry B 2013, 117 (27), 8061-8074.
Qian, B.; Montiel, D.; Bregulla, A.; Cichos, F.; Yang, H., "Harnessing thermal fluctuations for purposeful activities: the manipulation of single micro-swimmers by adaptive photon nudging." Chemical Science 2013, 4 (4), 1420-1429.
Welsher, K.; Yang, H.; Ieee, "Model-Free Analysis of Time-Dependent Single-Molecule Spectroscopy Dynamics of Biological Macromolecules." 2012; p 921-923.
Hanson, J. A.; Brokaw, J.; Hayden, C. C.; Chu, J.-W.; Yang, H., "Structural distributions from single-molecule measurements as a tool for molecular mechanics." Chemical Physics 2012, 396, 61-71.
Tan, Y.-W.; Yang, H., "Seeing the forest for the trees: fluorescence studies of single enzymes in the context of ensemble experiments." Physical Chemistry Chemical Physics 2011, 13 (5), 1709-1721.
Hsia, C.-H.; Wuttig, A.; Yang, H., "An Accessible Approach to Preparing Water-Soluble Mn2+-Doped (CdSSe)ZnS (Core)Shell Nanocrystals for Ratiometric Temperature Sensing." Acs Nano 2011, 5 (12), 9511-9522.
Yang, J.-M.; Yang, H.; Lin, L., "Quantum Dot Nano Thermometers Reveal Heterogeneous Local Thermogenesis in Living Cells." Acs Nano 2011, 5 (6), 5067-5071.
Yang, H., "Analysis of Large-Amplitude Conformational Transition Dynamics in Proteins at the Single-Molecule Level." 2011; p 199-219.
Duderstadt, K. E.; Mott, M. L.; Crisona, N. J.; Chuang, K.; Yang, H.; Berger, J. M., "Origin Remodeling and Opening in Bacteria Rely on Distinct Assembly States of the DnaA Initiator." Journal of Biological Chemistry 2010, 285 (36), 28229-28239.
Flynn, E. M.; Hanson, J. A.; Alber, T.; Yang, H., "Dynamic Active-Site Protection by the M. tuberculosis Protein Tyrosine Phosphatase PtpB Lid Domain." Journal of the American Chemical Society 2010, 132 (13), 4772-4780.
Chen, B.; Sysoeva, T. A.; Chowdhury, S.; Guo, L.; De Carlo, S.; Hanson, J. A.; Yang, H.; Nixon, B. T., "Engagement of Arginine Finger to ATP Triggers Large Conformational Changes in NtrC1 AAA+ ATPase for Remodeling Bacterial RNA Polymerase." Structure 2010, 18 (11), 1420-1430.
Yang, H., "Progress in single-molecule spectroscopy in cells." Current Opinion in Chemical Biology 2010, 14 (1), 3-9.
Montiel, D.; Yang, H., "Real-time three-dimensional single-particle tracking spectroscopy for complex systems." Laser & Photonics Reviews 2010, 4 (3), 374-385.
Holman, H.-Y. N.; Miles, R.; Hao, Z.; Wozei, E.; Anderson, L. M.; Yang, H., "Real-Time Chemical Imaging of Bacterial Activity in Biofilms Using Open-Channel Microfluidics and Synchrotron FTIR Spectromicroscopy." Analytical Chemistry 2009, 81 (20), 8564-8570.
Yang, H., "The Orientation Factor in Single-Molecule Forster-Type Resonance Energy Transfer, with Examples for Conformational Transitions in Proteins." Israel Journal of Chemistry 2009, 49 (3-4), 313-321.