Yann Chemla

For More Information

• NSF Science and Technology Center for Quantitative Cell Biology
• Chemla group website

Education

• Ph.D., Physics, University of California-Berkeley, 2001

Biography

Professor Yann Chemla received his PhD. in physics from the University of California, Berkeley in 2001. Trained as a condensed matter experimentalist, he developed an interest in biophysics through his study of magnetotactic bacteria and his development of a magnetic nanoparticle-based biosensor. Prof. Chemla completed his transition to biophysics as a postdoctoral fellow in Prof. Carlos Bustamante’s laboratory at Berkeley. There, he trained in single-molecule methods, using optical tweezers to study DNA packaging in viruses. He joined the Department of Physics at the University of Illinois, Urbana-Champaign in 2007. He is the recipient of an NSF CAREER award and a Sloan Foundation Research Fellowship, and was named Fellow of the American Physical Society. He served as co-Director of the NSF Physics Frontiers Center (PFC) the “Center for the Physics of Living Cells” (CPLC) from 2015 to 2022.

Research Statement

The living cell is a remarkable “factory” of complex molecular structures that carry out specialized mechanical tasks and act like nano-scale machines. These molecular machines are involved in a wide range of biological processes, from faithfully copying the genome to propelling cells. Broadly speaking, the Chemla group is interested in understanding the mechanism by which these machines operate, interact with other cellular molecules, and are regulated. One area of focus is the proteins that process and maintain genomic DNA.

Our lab uses powerful biophysical techniques to follow these processes one molecule at a time, avoiding the averaging artifacts of traditional ensemble methods. Optical traps—or “optical tweezers”—which utilize the force generated by focused laser light to manipulate microscopic objects, allow us to follow the trajectories of individual molecules in real time and measure the forces they generate.

Research in the Chemla lab involves developing new methodologies and, enabled by these advances, making scientific discoveries. Examples include the developments of high-resolution optical tweezers to detect the Ångström-scale motion of proteins on DNA and of combined optical trap-fluorescence microscopy to investigate conformational dynamics in a DNA processing machine. Our group has further extended these approaches to study the fusion of subcellular protein condensates, cargo transport inside the cell, and the dynamics of individual swimming bacterial cells.

Members of the Chemla laboratory work on all facets of research in this area: design and construction of state-of-the art instrumentation, investigation of biological systems using single-molecule manipulation methods, and quantitative analysis and modeling of collected trajectories. Interested students and postdocs with backgrounds in physics, biology, chemistry, or related fields are welcome to contact me.

Undergraduate Research Opportunities

The Chemla group welcomes talented, motivated undergraduates to work in the lab. Past students have worked on projects in instrumentation and technique development, measurements on biological systems, and quantitative analysis/modeling. No prior experience in biophysics is required. Interested undergraduates should contact me directly to discuss research opportunities in the lab.

Selected Articles in Journals

• Ravan A, Procopio S, Chemla YR, Gruebele M. (2024) "Temperature-jump microscopy and interaction of Hsp70 heat shock protein with a client protein in vivo." Methods. 231:154-164.
• Nguyen, T.V.P., Wu, Y., Yao, T., Trinh, J.T., Zeng, L., Chemla, Y.R., Golding, I. (2024) "Co-infecting phages impede each other’s entry into the cell" Current Biol. 34(13):2841-2853
• Bano, R., Mears, P., Golding, I., Chemla, Y.R. (2023) "Flagellar dynamics reveal fluctuations and kinetic limit in the Escherichia coli chemotaxis network." Sci Rep. 13(1):22891
• Lu, S., Chemla, Y.R. (2023) "Optical traps induce fluorophore photobleaching by two-photon excitation." Biophys. J. 122(22):4316-4325
• Ravan, A., Feng, R., Gruebele, M., Chemla, Y.R. (2023) "Rapid automated 3-D pose estimation of larval zebrafish using a physical model-trained neural network." PLoS Comput Biol. 2023 19(10):e1011566
• Bobrovnikov, D., Makurath, M., Wolfe, C., Chemla, Y.R., Ha, T. (2023) "Helicase activity modulation with on-demand light-based conformational control." J Am Chem Soc. 145(39):21253-21262
• Carney S.P., Ma W., Whitley K.D., Jia H., Lohman T.M., Luthey-Schulten Z., Chemla Y.R. (2021) "Kinetic and structural mechanism for DNA unwinding by a non-hexameric helicase." Nat Commun. 12(1):7015. doi: 10.1038/s41467-021-27304-6.
• Dai L., Singh D., Lu S., Kottadiel V.I., Vafabakhsh R., Mahalingam M., Chemla Y.R., Ha T., Rao V.B. (2021) "A viral genome packaging ring-ATPase is a flexibly coordinated pentamer." Nat Commun. 12(1):6548. doi: 10.1038/s41467-021-26800-z.
• Stekas B., Yeo S., Troitskaia A., Honda M., Sho S., Spies M., Chemla Y.R. (2021) "Switch-like control of helicase processivity by single-stranded DNA binding protein." Elife 10:e60515.
• Rhine K., Makurath M.A., Liu J., Skanchy S., Lopez C., Catalan K.F., Ma Y., Fare C.M., Shorter J., Ha T., Chemla Y.R., Myong S. (2020) "ALS/FTLD-Linked Mutations in FUS Glycine Residues Cause Accelerated Gelation and Reduced Interactions with Wild-Type FUS." Mol Cell. 80(4):666-681.e8.
• Mitra J., Makurath M.A., Ngo T.T.M., Troitskaia A., Chemla Y.R., Ha T. (2019) "Extreme mechanical diversity of human telomeric DNA revealed by fluorescence-force spectroscopy." Proc Natl Acad Sci U S A. 116(17):8350-8359
• Makurath M.A., Whitley K.D., Nguyen B., Lohman T.M., Chemla Y.R. (2019) "Regulation of Rep helicase unwinding by an auto-inhibitory subdomain." Nucleic Acids Res. 47(5):2523-2532.
• Whitley K.D., Comstock M.J., Chemla Y.R. (2018) "Ultrashort Nucleic Acid Duplexes Exhibit Long Wormlike Chain Behavior with Force-Dependent Edge Effects" Phys. Rev. Lett. 120, 068102
• Whitley K.D., Comstock M.J., Chemla Y.R. (2017) "Elasticity of the transition state for oligonucleotide hybridization." Nucleic Acids Res. 45(2):547-555.
• Suksombat S., Khafizov R., Kozlov A.G., Lohman T.M., Chemla Y.R. (2015) "Structural dynamics of E. coli single-stranded DNA binding protein reveal DNA wrapping and unwrapping pathways." eLife, 4:e08193
• Comstock M.J., Whitley K.D., Jia H., Sokoloski J., Lohman T.M., Ha T., Chemla Y.R. (2015) "Direct observation of structure-function relationship in a nucleic acid-processing enzyme" Science 348(6232):352-354
• Arslan S., Khafizov R., Thomas C.D., Chemla Y.R., Ha T. (2015) "Engineering of a superhelicase through conformational control" Science 348(6232):344-347
• Mears, P.J., Koirala, S., Rao, C.V., Golding, I., Chemla, Y.R. (2014) "Escherichia coli swimming is robust against variations in flagellar number" eLife, 3:e01916
• Qi, Z., Pugh, R., Spies. M., Chemla, Y.R. (2013) "Sequence-Dependent Base-Pair Stepping Dynamics in XPD Helicase Unwinding" eLife, 2:e00334
• Kottadiel, V.I., Rao, V.B., Chemla, Y.R. (2012) "The dynamic pause-unpackaging state, an off-translocation recovery state of a DNA packaging motor from bacteriophage T4", PNAS 109(49):20000-5
• Min, T.L., Mears, P.J., Golding, I., and Chemla, Y.R. (2012) "Chemotactic adaptation kinetics of individual Escherichia coli cells", PNAS, 109(25):9869-74
• Comstock, M.J., Ha, T., Chemla, Y.R. (2011) "Ultrahigh-resolution optical trap with single-fluorophore sensitivity" Nature Methods. 8(4):335-40
• Min, T.L. Mears, P.J., Chubiz, L.M., Rao, C.V., Golding, I., Chemla, Y.R., (2009) "High-resolution, long-term characterization of bacterial motility using optical tweezers" Nature Methods. 6(11):831-835