Recent Publications
Bano, R., Mears, P., Golding, I., Chemla, Y.R. (2023). “Flagellar dynamics reveal fluctuations and kinetic limit in the Escherichia coli chemotaxis network” Scientific Reports, 13(1):22891
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 Computational Biology, 19(10):e1011566.
Lu, S., Chemla, Y.R. (2023). “Optical traps induce fluorophore photobleaching by two-photon excitation” Biophysical Journal, 122(22):4316-4325
Bobrovnikov, D., Makurath, M., Wolfe, C., Chemla, Y.R., Ha, T. (2023). “Helicase activity modulation with on-demand light-based conformational control” Journal of the American Chemical Society, 145(39):21253-21262
Shukla, S., Troitskaia, A., Swarna, N., Maity, B. K., Tjioe, M., Bookwalter, C. S., Trybus, K., Chemla, Y.R. and Selvin, P. (2022). “High-throughput force measurement of individual kinesin-1 motors during multi-motor transport” Nanoscale, doi:10.1039/D2NR01701F
Carney, S.P., Ma, W., Whitley, K.D., Jia, H., Lohman, T.M., Luthey-Schulten, Z. and Chemla, Y.R., (2021) “Kinetic and structural mechanism for DNA unwinding by a non-hexameric helicase” Nature Communications, doi:10.1038/s41467-021-27304-6
Dai, L., Singh, D., Lu, S., Kottadiel, V., Vafabakhsh, R., Mahalingam, M., Chemla, Y.R., Ha, T. and Rao, V.B., (2021) “A viral genome packaging ring-ATPase is a flexibly coordinated pentamer” Nature Communications, doi:10.1038/s41467-021-26800-z
Stekas, B., Yeo, S., Troitskaia, A., Honda, M., Sho, S., Spies, M. and Chemla, Y.R., (2021) “Switch-like control of helicase processivity by single-stranded DNA binding protein” eLife, doi:10.7554/eLife.60515
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” Molecular cell, doi:10.1016/j.molcel.2020.10.014
Tjioe, M., Shukla, S., Vaidya, R., Troitskaia, A., Bookwalter, C.S., Trybus, K.M., Chemla, Y.R. and Selvin, P.R., (2019) “Multiple kinesins induce tension for smooth cargo transport” eLife, doi:10.7554/eLife.50974
Perlova, T., Gruebele, M., Chemla, Y.R., (2019) “Blue Light Is a Universal Signal for Escherichia coli Chemoreceptors” Journal of bacteriology, doi:10.1128/JB.00762-18
Mitra, J., Makurath, M.A., Ngo, T.T., Troitskaia, A., Chemla, Y.R., Ha, T., (2019) “Extreme mechanical diversity of human telomeric DNA revealed by fluorescence-force spectroscopy” Proceedings of the National Academy of Science, doi:10.1073/pnas.1815162116
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 Research, doi:10.1093/nar/gkz023
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, doi:10.1103/PhysRevLett.120.068102
Ma, W., Whitley, K.D., Chemla, Y.R., Luthey-Schulten, Z., Schulten, K., (2018) “Free energy simulations reveal molecular mechanism for functional switch of a DNA helicase” eLife, doi:10.7554/eLife.34186
Lin, S., Alam, T.I., Kottadiel, V.I., VanGessel, C.J., Tang, W.-C., Chemla, Y.R., Rao, V.B., (2017) “Altering the Speed of a DNA Packaging Motor from Bacteriophage T4” Nucleic Acids Research, doi:10.1093/nar/gkx809
Li, I.T.S., Ha, T., Chemla, Y.R., (2017) “Mapping cell surface adhesion by rotation tracking and adhesion footprinting” Scientific Reports, doi: 10.1038/srep44502
Whitley, K.D., Comstock, M.J., Chemla, Y.R., (2017) “Elasticity of the transition state for oligonucleotide hybridization” Nucleic Acids Research, doi:10.1093/nar/gkw1173
Chowdhury, F., Li, I.T., Ngo, T.T., Leslie, B.J., Kim, B.C., Sokoloski, J.E., Weiland, E., Wang, X., Chemla, Y.R., Lohman, T.M. and Ha, T., (2016) “Defining single molecular forces required for Notch activation using Nano Yoyo” Nano Letters, doi:10.1021/acs.nanolett.6b01403
Wang, X., Rahil, Z., Li, I.T., Chowdhury, F., Leckband, D.E., Chemla, Y.R. and Ha, T., (2016) “Constructing modular and universal single molecule tension sensor using protein G to study mechano-sensitive receptors” Scientific Reports, doi:10.1038/srep21584
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, doi:10.7554/eLife.08193
Girdhar, K., Gruebele, M., Chemla, Y.R., (2015) “The Behavioral Space of Zebrafish Locomotion and Its Neural Network Analog” PLoS One, doi:10.1371/journal.pone.0128668
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 Cprocessing enzyme” Science, doi:10.1126/science.aaa0130
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, doi:10.7554/eLife.01916
Qi, Z., Pugh, R.A., Spies, M., Chemla, Y.R., (2013) “Sequence-dependent base pair stepping dynamics in XPD helicase unwinding” eLife, doi:10.7554/eLife.00334
Blehm, B.H., Schroer, T.A., Trybus, K.M., Chemla, Y.R., Selvin, P.R., (2013) “In vivo optical trapping indicates kinesin's stall force is reduced by dynein during intracellular transport” Proc. Natl. Acad. Sci., 110(9):3381-6
Landry, M.P., Zou, X., Wang, L., Huang, W.M., Schulten, K., Chemla, Y.R., (2013) “DNA target sequence identification mechanism for dimer-active protein complexes” Nucleic Acids Res, 41(4):2416-27
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” Proc. Natl. Acad. Sci., 109(49):20000-5
Min, T.L., Mears, P.J., Golding, I., Chemla, Y.R., (2012) “Chemotactic adaptation kinetics of individual Escherichia coli cells” Proc. Natl. Acad. Sci., 109(25):9869-74
Girdhar, K., Scott, G., Chemla Y.R., Gruebele, M., (2011) “Better biomolecule thermodynamics from kinetics” J. Chem. Phys., 135(1):015102
Zhang, Z., Kottadiel, V.I., Vafabakhsh, R., Dai, L., Chemla, Y.R., Ha, T., Rao, V.B., (2011) “A promiscuous DNA packaging machine from bacteriophage t4” PLoS Biol, 9(2), e1000592
Comstock, M.J., Ha, T., Chemla, Y.R., (2011) “Ultrahigh-resolution optical trap with single-fluorophore sensitivity” Nature Methods, 8, 335-340
Saini, S., Koirala, S., Floess, E., Mears, P.J., Chemla, Y.R., Golding, I., Aldridge, C., Aldridge, P.D., Rao, C.V. (2010), “FliZ Induces a Kinetic Switch in Flagellar Gene Expression” Journal of Bacteriology, 192(24), 6477-81
Liu, Y., Park, J., Dahmen, K.A., Chemla, Y.R., Ha, T.,(2010) “A comparative study of multivariate and univariate hidden Markov modelings in time-binned single-molecule FRET data analysis” J. Phys. Chem. B., 114(16):5386-403
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, 831-5
Landry, M.P., McCall, P.M., Qi, Z., Chemla, Y.R. (2009) “Characterization of photoactivated singlet oxygen damage in single-molecule optical trap experiments”, Biophys. J., 97, 2128-36
Recent Reviews
Bustamante, C.J., Chemla, Y.R., Liu, S. and Wang, M.D., (2021) “Optical tweezers in single-molecule biophysics” Nature Reviews Methods Primers, doi:10.1038/s43586-021-00027-0
Whitley, K.D., Comstock, M.J., Chemla, Y.R., (2017) “High-resolution Optical Tweezers Combined with Single-Molecule Confocal Microscopy” chapter in Methods in Enzymology: Single-molecule enzymology, doi:10.1016/bs.mie.2016.10.036
Whitley, K.D., Comstock, M.J., Chemla, Y.R., (2016) “High-resolution "Fleezers": Dual-trap optical tweezers combined with Single-molecule Fluorescence Detection” Methods in Molecular Biology, doi:10.1007/978-1-4939-6421-5_8
Chemla, Y.R., (2016) “High-resolution, Hybrid Optical Trapping Methods and their Application to Nucleic Acid Processing Proteins” Biopolymers, doi:10.1002/bip.22880
Chemla, Y.R., Smith, D.E., (2011) “Single-molecule studies of viral DNA packaging” in Viral Molecular Machines (V. Rao & M. Rossman, eds.), Springer, New York, NY.
Moffitt, J.R., Chemla, Y.R., Bustamante, C. (2010) “Methods in Statistical Kinetics” Methods Enzymol. 475:221-57
Chemla, Y.R. (2010) “Revealing the base pair stepping dynamics of nucleic acid motor proteins with optical traps” Phys Chem. Chem Phys
Moffitt, J.R., Chemla, Y.R., Smith, S.B., Bustamante, C. (2008) “Recent Advances in Optical Tweezers” Annu Rev Biochem. 77, 19-1:19-24
Bustamante, C., Chemla, Y.R., Moffitt, J.R. (2007) “High resolution dual trap optical tweezers with differential detection” in Single Molecule Techniques: A Laboratory Manual (P. Selvin & T.J. Ha, eds.) Cold Spring Harbor Laboratory Press, Woodbury NY., pp. 297-324
Bustamante, C., Chemla, Y.R., Forde, N., Izhaky, D. (2004) “Mechanical processes in biochemistry” Ann. Rev. Biochem. 73, 705-48
Publications (prior to becoming Professor)
Moffitt, J.R., Chemla, Y.R., Bustamante, C., (2010) “Mechanistic constraints from the substrate concentration dependence of enzymatic fluctuations” Proc. Natl. Acad. Sci, 107, 15739-44
Aathavan, K., Politzer, A.T., Kaplan, A., Moffitt, J.R., Chemla, Y.R., Grimes, S., Jardine, P.J., Anderson, D.L., Bustamante, C. (2009) “Substrate Interactions and Promiscuity in a Viral DNA Packaging Motor” Nature., 461, 669-673
Ibarra, B., Chemla, Y.R., Plyasunov, S., Smith, S.B., Lázaro, J.M., Salas, M., Bustamante, C. (2009) “Proofreading dynamics of a processive DNA polymerase” , EMBO. J., 28, 2794-802
Moffitt, J.R., Chemla, Y.R., Aathavan, K., Grimes, S., Jardine, P.J., Anderson, D.L., Bustamante, C. (2009). “Intersubunit coordination in a homomeric ring ATPase” Nature., 457, 446-450
Chemla, Y.R., Moffitt, J.R., Bustamante, C. (2008) “Exact solutions for kinetic models of macromolecular dynamics” J. Phys. Chem. B, 112(19):6025-6044
Moffitt, J.R., Chemla, Y.R., Izhaky, D., Bustamante, C. (2006) “Differential detection of dual traps improves the spatial resolution of optical tweezers” Proc. Natl. Acad. Sci, 103, 9006-9011
Chemla, Y.R., Karunakaran, A., Michaelis, J., Grimes, S., Jardine, P.J., Anderson, D.L., Bustamante, C. (2005) “Mechanism of force generation of a viral DNA packaging motor” Cell , 122, 683-692
Lee, S., Myers, W.R., Grossman, H.L., Cho, H.M., Chemla, Y.R. and Clarke, J. (2002) “Magnetic gradiometer based on a high-transition temperature superconducting quantum interference device for improved sensitivity of a biosensor” Applied physics letters, doi:10.1063/1.1515122
Chemla, Y.R., Grossman, H.L., Poon, Y., McDermott, R., Stevens, R., Alper, M.D. and Clarke, J. (2000) “Ultrasensitive magnetic biosensor for homogeneous immunoassay” Proc. Natl. Acad. Sci., doi:10.1073/pnas.97.26.14268
Chemla, Y.R., Grossman, H.L., Lee, T.S., Clarke, J., Adamkiewicz, M. and Buchanan, B.B. (1999) “A new study of bacterial motion: Superconducting quantum interference device microscopy of magnetotactic bacteria” Biophysical journal, doi:10.1016/S0006-3495(99)77485-0
Lee, T.S., Chemla, Y.R., Dantsker, E., Clarke, J., (1997) “High-T-c SQUID microscope for room temperature samples” IEEE TRANSACTIONS ON APPLIED SUPERCONDUCTIVITY, doi:10.1109/77.621999