Chemla Research Group
Recent Publications
Bano, R., Mears, P., Golding, I., Chemla, Y.R. (2023). “Flagellar dynamics reveal fluctuations and kinetic limit in the Escherichia coli chemotaxis networkScientific 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 networkPLoS Computational Biology, 19(10):e1011566.
Lu, S., Chemla, Y.R. (2023). “Optical traps induce fluorophore photobleaching by two-photon excitationBiophysical 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 controlJournal 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 transportNanoscale, 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 helicaseNature 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 pentamerNature 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 proteineLife, 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 FUSMolecular 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 transporteLife, doi:10.7554/eLife.50974
Perlova, T., Gruebele, M., Chemla, Y.R., (2019) “Blue Light Is a Universal Signal for Escherichia coli ChemoreceptorsJournal 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 spectroscopyProceedings 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 subdomainNucleic 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 EffectsPhys 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 helicaseeLife, 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 T4Nucleic 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 footprintingScientific Reports, doi: 10.1038/srep44502
Whitley, K.D., Comstock, M.J., Chemla, Y.R., (2017) “Elasticity of the transition state for oligonucleotide hybridizationNucleic 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 YoyoNano 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 receptorsScientific 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 pathwayseLife, doi:10.7554/eLife.08193
Girdhar, K., Gruebele, M., Chemla, Y.R., (2015) “The Behavioral Space of Zebrafish Locomotion and Its Neural Network AnalogPLoS 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 enzymeScience, 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 numbereLife, 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 unwindingeLife, 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 transportProc. 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 complexesNucleic 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 T4Proc. 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 cellsProc. Natl. Acad. Sci., 109(25):9869-74
Girdhar, K., Scott, G., Chemla Y.R., Gruebele, M., (2011) “Better biomolecule thermodynamics from kineticsJ. 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 t4PLoS Biol, 9(2), e1000592
Comstock, M.J., Ha, T., Chemla, Y.R., (2011) “Ultrahigh-resolution optical trap with single-fluorophore sensitivityNature 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 ExpressionJournal 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 analysisJ. 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 tweezersNature 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 biophysicsNature 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 Microscopychapter 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 DetectionMethods in Molecular Biology, doi:10.1007/978-1-4939-6421-5_8
Chemla, Y.R., Smith, D.E., (2011) “Single-molecule studies of viral DNA packagingin Viral Molecular Machines (V. Rao & M. Rossman, eds.), Springer, New York, NY.
Moffitt, J.R., Chemla, Y.R., Bustamante, C. (2010) “Methods in Statistical KineticsMethods Enzymol. 475:221-57
Moffitt, J.R., Chemla, Y.R., Smith, S.B., Bustamante, C. (2008) “Recent Advances in Optical TweezersAnnu Rev Biochem. 77, 19-1:19-24
Bustamante, C., Chemla, Y.R., Moffitt, J.R. (2007) “High resolution dual trap optical tweezers with differential detectionin 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 biochemistryAnn. 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 fluctuationsProc. 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 MotorNature., 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 ATPaseNature., 457, 446-450
Chemla, Y.R., Moffitt, J.R., Bustamante, C. (2008) “Exact solutions for kinetic models of macromolecular dynamicsJ. 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 tweezersProc. 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