Yann Robert Chemla

1993 …2019
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Research Output 1993 2019

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2019

Blue light is a universal signal for Escherichia coli chemoreceptors

Perlova, T., Gruebele, M. H. W. & Chemla, Y. R., Jan 1 2019, In : Journal of bacteriology. 201, 11, e0076218.

Research output: Contribution to journalArticle

Escherichia coli
Light
Bacteria
Proton-Motive Force
Tars

Extreme mechanical diversity of human telomeric DNA revealed by fluorescence-force spectroscopy

Mitra, J., Makurath, M. A., Ngo, T. T. M., Troitskaia, A., Chemla, Y. R. & Ha, T., Jan 1 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 17, p. 8350-8359 10 p.

Research output: Contribution to journalArticle

G-Quadruplexes
Fluorescence Spectrometry
DNA
Optical Tweezers
Fluorescence Resonance Energy Transfer

Regulation of Rep helicase unwinding by an auto-inhibitory subdomain

Makurath, M. A., Whitley, K. D., Nguyen, B., Lohman, T. M. & Chemla, Y. R., Jan 1 2019, In : Nucleic acids research. 47, 5, p. 2523-2532 10 p.

Research output: Contribution to journalArticle

Open Access
Optical Tweezers
Nucleic Acids
Maintenance
Escherichia coli
DNA
2018

Free-energy simulations reveal molecular mechanism for functional switch of a DNA helicase

Ma, W., Whitley, K. D., Chemla, Y. R., Luthey-Schulten, Z. A. & Schulten, K., Apr 17 2018, In : eLife. 7, e34186.

Research output: Contribution to journalArticle

DNA Repair Enzymes
DNA Helicases
Computational Biology
Nucleic Acids
Free energy

Optical Control of Metal Ion Probes in Cells and Zebrafish Using Highly Selective DNAzymes Conjugated to Upconversion Nanoparticles

Yang, Z., Loh, K. Y., Chu, Y. T., Feng, R., Satyavolu, N. S. R., Xiong, M., Nakamata Huynh, S. M., Hwang, K., Li, L., Xing, H., Zhang, X., Chemla, Y. R., Gruebele, M. H. W. & Lu, Y., Dec 19 2018, In : Journal of the American Chemical Society. 140, 50, p. 17656-17665 10 p.

Research output: Contribution to journalArticle

Catalytic DNA
Zebrafish
Nanoparticles
Metal ions
Metals

Ultrashort Nucleic Acid Duplexes Exhibit Long Wormlike Chain Behavior with Force-Dependent Edge Effects

Whitley, K. D., Comstock, M. J. & Chemla, Y. R., Feb 9 2018, In : Physical review letters. 120, 6, 068102.

Research output: Contribution to journalArticle

nucleic acids
nanotechnology
biology
2017

Altering the speed of a DNA packaging motor from bacteriophage T4

Lin, S., Alam, T. I., Kottadiel, V. I., Vangessel, C. J., Tang, W. C., Chemla, Y. R. & Rao, V. B., Jan 1 2017, In : Nucleic acids research. 45, 19, p. 11437-11448 12 p.

Research output: Contribution to journalArticle

DNA Packaging
Bacteriophage T4
Adenosine Triphosphatases
Product Packaging
Mutagenesis

Elasticity of the transition state for oligonucleotide hybridization

Whitley, K. D., Comstock, M. J. & Chemla, Y. R., Jan 1 2017, In : Nucleic acids research. 45, 2, p. 547-555 9 p.

Research output: Contribution to journalArticle

Elasticity
Oligonucleotides
Base Pairing
Optical Tweezers
Nucleic Acid Hybridization

Mapping cell surface adhesion by rotation tracking and adhesion footprinting

Li, I. T. S., Ha, T. & Chemla, Y. R., Mar 14 2017, In : Scientific Reports. 7, 44502.

Research output: Contribution to journalArticle

Cell Adhesion
Membranes
Surface Properties
Adhesives
Leukemia
2016

Constructing modular and universal single molecule tension sensor using protein G to study mechano-sensitive receptors

Wang, X., Rahil, Z., Li, I. T. S., Chowdhury, F., Leckband, D. E., Chemla, Y. R. & Ha, T., Feb 15 2016, In : Scientific reports. 6, 21584.

Research output: Contribution to journalArticle

Ligands
Proteins
Cadherins
P-Selectin
Gravitation

Defining single molecular forces required for notch activation using nano yoyo

Chowdhury, F., Li, I. T. S., Ngo, T. T. M., Leslie, B. J., Kim, B. C., Sokoloski, J. E., Weiland, E., Wang, X., Chemla, Y. R., Lohman, T. M. & Ha, T., Jun 8 2016, In : Nano letters. 16, 6, p. 3892-3897 6 p.

Research output: Contribution to journalArticle

notches
DNA
Chemical activation
activation
Single-Stranded DNA
2015

Direct observation of structure-function relationship in a nucleic acid -processing enzyme

Comstock, M. J., Whitley, K. D., Jia, H., Sokoloski, J., Lohman, T. M., Ha, T. & Chemla, Y. R., Apr 17 2015, In : Science. 348, 6232, p. 352-354 3 p.

Research output: Contribution to journalArticle

Optical Tweezers
DNA Helicases
Fluorescence Microscopy
DNA Repair
Nucleic Acids

Engineering of a superhelicase through conformational control

Arslan, S., Khafizov, R., Thomas, C. D., Chemla, Y. R. & Ha, T., Apr 17 2015, In : Science. 348, 6232, p. 344-347 4 p.

Research output: Contribution to journalArticle

Base Pairing
Nucleic Acids

Structural dynamics of E. Coli singlestranded DNA binding protein reveal DNA wrapping and unwrapping pathways

Suksombat, S., Khafizov, R., Kozlov, A. G., Lohman, T. M. & Chemla, Y. R., Aug 25 2015, In : eLife. 4, AUGUST2015, e08193.

Research output: Contribution to journalArticle

Structural dynamics
DNA-Binding Proteins
Escherichia coli
DNA
Recombinases

The behavioral space of zebrafish locomotion and its neural network analog

Girdhar, K., Gruebele, M. & Chemla, Y. R., Jul 1 2015, In : PloS one. 10, 7, e0128668.

Research output: Contribution to journalArticle

Zebrafish
Locomotion
Danio rerio
Fish
neural networks
2014

A nutrient-tunable bistable switch controls motility in Salmonella enterica serovar Typhimurium

Koirala, S., Mears, P., Sim, M., Golding, I., Chemla, Y. R., Aldridge, P. D. & Rao, C. V., Aug 26 2014, In : mBio. 5, 5, e01611-14.

Research output: Contribution to journalArticle

Salmonella enterica
Food
Bacteria
Flagella
Growth

Escherichia coli swimming is robust against variations in flagellar number

Mears, P. J., Koirala, S., Rao, C. V., Golding, I. & Chemla, Y. R., Feb 11 2014, In : eLife. 2014, 3, e01916.

Research output: Contribution to journalArticle

Flagella
Escherichia coli
Chemotaxis
Swimming
2013

DNA target sequence identification mechanism for dimer-Active protein complexes

Landry, M. P., Zou, X., Wang, L., Huang, W. M., Schulten, K. & Chemla, Y. R., Feb 1 2013, In : Nucleic acids research. 41, 4, p. 2416-2427 12 p.

Research output: Contribution to journalArticle

DNA
Proteins
Recombinases
Nucleoproteins
DNA-Binding Proteins

In vivo optical trapping indicates kinesin's stall force is reduced by dynein during intracellular transport

Blehm, B. H., Schroer, T. A., Trybus, K. M., Chemla, Y. R. & Selvin, P. R., Feb 26 2013, In : Proceedings of the National Academy of Sciences of the United States of America. 110, 9, p. 3381-3386 6 p.

Research output: Contribution to journalArticle

Optical Tweezers
Dyneins
Kinesin
Cytoplasmic Dyneins
In Vitro Techniques

Sequence-dependent base pair stepping dynamics in XPD helicase unwinding

Qi, Z., Pugh, R. A., Spies, M. & Chemla, Y. R., May 28 2013, In : eLife. 2013, 2, e00334.

Research output: Contribution to journalArticle

Base Pairing
DNA Helicases
DNA
Optical tweezers
Transcription
2012

Chemotactic adaptation kinetics of individual Escherichia coli cells

Min, T. L., Mears, P. J., Golding, I. & Chemla, Y. R., Jun 19 2012, In : Proceedings of the National Academy of Sciences of the United States of America. 109, 25, p. 9869-9874 6 p.

Research output: Contribution to journalArticle

Escherichia coli
Optical Tweezers
Chemotactic Factors
Chemotaxis
Bacteria
DNA Packaging
Bacteriophage T4
Viral Genome
DNA
Adenosine Triphosphate
2011

A promiscuous DNA packaging machine from bacteriophage T4

Zhang, Z., Kottadiel, V. I., Vafabakhsh, R., Dai, L., Chemla, Y. R., Ha, T. & Rao, V. B., Feb 1 2011, In : PLoS biology. 9, 2, e1000592.

Research output: Contribution to journalArticle

Packaging machines
DNA Packaging
Bacteriophage T4
Bacteriophages
bacteriophages

Better biomolecule thermodynamics from kinetics

Girdhar, K., Scott, G., Chemla, Y. R. & Gruebele, M., Jul 7 2011, In : Journal of Chemical Physics. 135, 1, 015102.

Research output: Contribution to journalArticle

Biomolecules
Denaturation
biopolymer denaturation
Thermodynamics
Chromophores

Ultrahigh-resolution optical trap with single-fluorophore sensitivity

Comstock, M. J., Ha, T. & Chemla, Y. R., Apr 1 2011, In : Nature Methods. 8, 4, p. 335-340 6 p.

Research output: Contribution to journalArticle

Optical Tweezers
Fluorophores
Fluorescence
DNA
DNA-Binding Proteins
2010

A comparative study of multivariate and univariate hidden Markov modelings in time-binned single-molecule FRET data analysis

Liu, Y., Park, J., Dahmen, K. A., Chemla, Y. R. & Ha, T., Apr 29 2010, In : Journal of Physical Chemistry B. 114, 16, p. 5386-5403 18 p.

Research output: Contribution to journalArticle

Fluorescence
fluorescence
Molecules
Trajectories
trajectories

FliZ induces a kinetic switch in flagellar gene expression

Saini, S., Koirala, S., Floess, E., Mears, P. J., Chemla, Y. R., Golding, I., Aldridge, C., Aldridge, P. D. & Rao, C. V., Dec 1 2010, In : Journal of bacteriology. 192, 24, p. 6477-6481 5 p.

Research output: Contribution to journalArticle

Gene Expression
Salmonella enterica

Mechanistic constraints from the substrate concentration dependence of enzymatic fluctuations

Moffitt, J. R., Chemla, Y. R. & Bustamante, C., Sep 7 2010, In : Proceedings of the National Academy of Sciences of the United States of America. 107, 36, p. 15739-15744 6 p.

Research output: Contribution to journalArticle

Product Packaging
Enzymes
Bacteriophages
Nucleotides
Hot Temperature

Revealing the base pair stepping dynamics of nucleic acid motor proteins with optical traps

Chemla, Y. R., Mar 23 2010, In : Physical Chemistry Chemical Physics. 12, 13, p. 3080-3095 16 p.

Research output: Contribution to journalArticle

nucleic acids
Nucleic Acids
traps
proteins
ribosomes
2009

Characterization of photoactivated singlet oxygen damage in single-molecule optical trap experiments

Landry, M. P., McCall, P. M., Qi, Z. & Chemla, Y. R., Oct 21 2009, In : Biophysical journal. 97, 8, p. 2128-2136 9 p.

Research output: Contribution to journalArticle

Optical Tweezers
Singlet Oxygen
Microspheres
Polystyrenes
Lasers

High-resolution, long-term characterization of bacterial motility using optical tweezers

Min, T. L., Mears, P. J., Chubiz, L. M., Rao, C. V., Golding, I. & Chemla, Y. R., Oct 1 2009, In : Nature Methods. 6, 11, p. 831-835 5 p.

Research output: Contribution to journalArticle

Optical Tweezers
Optical tweezers
Assays
Cell Migration Assays
Controlled Environment

High-resolution dual-trap optical tweezers with differential detection: Instrument design

Bustamante, C., Chemla, Y. R. & Moffitt, J. R., Dec 7 2009, In : Cold Spring Harbor protocols. 4, 10

Research output: Contribution to journalArticle

Optical Tweezers
Optical tweezers
Biological systems
Noise
Optics

High-resolution dual-trap optical tweezers with differential detection: Managing environmental noise

Bustamante, C., Chemla, Y. R. & Moffitt, J. R., Dec 7 2009, In : Cold Spring Harbor protocols. 4, 10

Research output: Contribution to journalArticle

Optical Tweezers
Optical tweezers
Noise
Biological systems
Biological Phenomena

High-resolution dual-trap optical tweezers with differential detection: Data collection and instrument calibration

Bustamante, C., Chemla, Y. R. & Moffitt, J. R., Dec 7 2009, In : Cold Spring Harbor protocols. 4, 10

Research output: Contribution to journalArticle

Optical Tweezers
Optical tweezers
Calibration
Biological Phenomena
Noise
Optical Tweezers
Optical tweezers
Noise
Instrument components
Experiments

High-resolution dual-trap optical tweezers with differential detection: An introduction

Bustamante, C., Chemla, Y. R. & Moffitt, J. R., Dec 7 2009, In : Cold Spring Harbor Protocols. 4, 10

Research output: Contribution to journalArticle

Optical Tweezers
Optical tweezers
Biological Phenomena
Molecules
Mechanical properties

High-Resolution dual-trap optical tweezers with differential detection: Alignment of instrument components

Bustamante, C., Chemla, Y. R. & Moffitt, J. R., Dec 7 2009, In : Cold Spring Harbor protocols. 4, 10

Research output: Contribution to journalArticle

Instrument components
Optical Tweezers
Optical tweezers
Infrared radiation
Lasers

Intersubunit coordination in a homomeric ring ATPase

Moffitt, J. R., Chemla, Y. R., Aathavan, K., Grimes, S., Jardine, P. J., Anderson, D. L. & Bustamante, C., Jan 22 2009, In : Nature. 457, 7228, p. 446-450 5 p.

Research output: Contribution to journalArticle

Base Pairing
Adenosine Triphosphatases
Optical Tweezers
DNA Packaging
Chromosome Segregation

Proofreading dynamics of a processive DNA polymerase

Ibarra, B., Chemla, Y. R., Plyasunov, S., Smith, S. B., Lázaro, J. M., Salas, M. & Bustamante, C., Sep 16 2009, In : EMBO Journal. 28, 18, p. 2794-2802 9 p.

Research output: Contribution to journalArticle

DNA-Directed DNA Polymerase
Polymerization
DNA Primers
Exonucleases
Conformations

Substrate interactions and promiscuity in a viral DNA packaging motor

Aathavan, K., Politzer, A. T., Kaplan, A., Moffitt, J. R., Chemla, Y. R., Grimes, S., Jardine, P. J., Anderson, D. L. & Bustamante, C., Oct 1 2009, In : Nature. 461, 7264, p. 669-673 5 p.

Research output: Contribution to journalArticle

DNA Packaging
Virus Assembly
Viral DNA
DNA
Product Packaging
2008

Exact solutions for kinetic models of macromolecular dynamics

Chemla, Y. R., Moffitt, J. R. & Bustamante, C., May 15 2008, In : Journal of Physical Chemistry B. 112, 19, p. 6025-6044 20 p.

Research output: Contribution to journalArticle

Molecules
Kinetics
kinetics
Molecular Motor Proteins
Nucleic acids
2006

Differential detection of dual traps improves the spatial resolution of optical tweezers

Moffitt, J. R., Chemla, Y. R., Izhaky, D. & Bustamante, C., Jun 13 2006, In : Proceedings of the National Academy of Sciences of the United States of America. 103, 24, p. 9006-9011 6 p.

Research output: Contribution to journalArticle

Optical Tweezers
Microspheres
2005

Mechanism of force generation of a viral DNA packaging motor

Chemla, Y. R., Aathavan, K., Michaelis, J., Grimes, S., Jardine, P. J., Anderson, D. L. & Bustamante, C., Sep 9 2005, In : Cell. 122, 5, p. 683-692 10 p.

Research output: Contribution to journalArticle

DNA Packaging
Virus Assembly
Viral DNA
Packaging
Adenosine Triphosphatases
2002

Magnetic gradiometer based on a high-transition temperature superconducting quantum interference device for improved sensitivity of a biosensor

Lee, S., Myers, W. R., Grossman, H. L., Cho, H. M., Chemla, Y. R. & Clarke, J., Oct 14 2002, In : Applied Physics Letters. 81, 16, p. 3094-3096 3 p.

Research output: Contribution to journalArticle

gradiometers
bioinstrumentation
transition temperature
interference
sensitivity
2000

Ultrasensitive magnetic biosensor for homogeneous immunoassay

Chemla, Y. R., Grossman, H. L., Poon, Y., McDermott, R., Stevens, R., Alper, M. D. & Clarke, J., Dec 19 2000, In : Proceedings of the National Academy of Sciences of the United States of America. 97, 26, p. 14268-14272 5 p.

Research output: Contribution to journalArticle

Biosensing Techniques
Immunoassay
Nanoparticles
Equipment and Supplies
Atmospheric Pressure
1999

A new study of bacterial motion: Superconducting quantum interference device microscopy of magnetotactic bacteria

Chemla, Y. R., Grossman, H. L., Lee, T. S., Clarke, J., Adamkiewicz, M. & Buchanan, B. B., Jun 1999, In : Biophysical journal. 76, 6, p. 3323-3330 8 p.

Research output: Contribution to journalArticle

Interference Microscopy
Bacteria
Equipment and Supplies
Magnetic Fields
Temperature
1997

High-tc squid microscope for room temperature samples

Lee, T. S., Chemla, Y. R., Dantsker, E. & Clarke, J., Dec 1 1997, In : IEEE Transactions on Applied Superconductivity. 7, 2 PART 3, p. 3147-3150 4 p.

Research output: Contribution to journalArticle

SQUIDs
Microscopes
microscopes
room temperature
silicon nitrides
1993

Wavelength variation of laser emission along the entire rim of slightly deformed microdroplets

Chen, G., Hill, S. C., Mazumder, M. M., Chemla, Y. R., Serpengüzel, A. & Chang, R. K., Dec 1993, In : Optics Letters. 18, 23, p. 1993-1995 3 p.

Research output: Contribution to journalArticle

rims
spectrographs
wavelengths
lasers
slits