JILA Science Publications
Displaying 1 - 62 of 62
2024
Quantifying a light-induced energetic change in bacteriorhodopsin by force spectroscopy
David Jacobson, Thomas Perkins, Proceedings of the National Academy of Sciences 121, e2313818121 (2024).
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David Jacobson, Thomas Perkins, Proceedings of the National Academy of Sciences 121, e2313818121 (2024).
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2022
Force-Activated DNA Substrates for In Situ Generation of ssDNA and Designed ssDNA/dsDNA Structures in an Optical-Trapping Assay
Arnulf Taylor, Stephen Okoniewski, Lyle Uyetake, Thomas Perkins, Methods in Biology , 273-312 (2022).
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Arnulf Taylor, Stephen Okoniewski, Lyle Uyetake, Thomas Perkins, Methods in Biology , 273-312 (2022).
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2021
Free-energy changes of bacteriorhodopsin point mutants measured by single-molecule force spectroscopy
David Jacobson, Thomas Perkins, Proceedings of the National Academy of Sciences 118, e2020083118 (2021).
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David Jacobson, Thomas Perkins, Proceedings of the National Academy of Sciences 118, e2020083118 (2021).
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Modulation of a protein-folding landscape revealed by AFM-based force spectroscopy notwithstanding instrumental limitations
Devin Edwards, Marc-Andre LeBlanc, Thomas Perkins, Proceedings of the National Academy of Sciences 118, e2015728118 (2021).
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Devin Edwards, Marc-Andre LeBlanc, Thomas Perkins, Proceedings of the National Academy of Sciences 118, e2015728118 (2021).
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Type III secretion system effector proteins are mechanically labile
Marc-Andre LeBlanc, Morgan Fink, Thomas Perkins, Marcelo Sousa, Proceedings of the National Academy of Sciences 118, e2019566118 (2021).
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Marc-Andre LeBlanc, Morgan Fink, Thomas Perkins, Marcelo Sousa, Proceedings of the National Academy of Sciences 118, e2019566118 (2021).
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2020
Correcting molecular transition rates measured by single-molecule force spectroscopy for limited temporal resolution
David Jacobson, Thomas Perkins, Physical Review E 102, 022402 (2020).
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David Jacobson, Thomas Perkins, Physical Review E 102, 022402 (2020).
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Quantifying the native energetics stabilizing bacteriorhodopsin by single-molecule force spectroscopy
Hao Yu, David Jacobson, Hao Luo, Thomas Perkins, Physical Review Letters 125, 068102 (2020).
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Hao Yu, David Jacobson, Hao Luo, Thomas Perkins, Physical Review Letters 125, 068102 (2020).
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Bending and looping of long DNA by polycomb repressive complex 2 revealed by AFM imaging in liquid
Patrick Heenan, Xueyin Wang, Anne Gooding, Thomas Cech, Thomas Perkins, Nucleic Acids Research 48, 2969-2981 (2020).
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Patrick Heenan, Xueyin Wang, Anne Gooding, Thomas Cech, Thomas Perkins, Nucleic Acids Research 48, 2969-2981 (2020).
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Membrane-protein unfolding intermediates detected with enhanced precision using a zigzag force ramp
David Jacobson, Lyle Uyetake, Thomas Perkins, Biophysical Journal 118, 667-675 (2020).
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David Jacobson, Lyle Uyetake, Thomas Perkins, Biophysical Journal 118, 667-675 (2020).
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2019
Imaging DNA equilibrated onto mica in liquid using biochemically relevant deposition conditions
Patrick Heenan, Thomas Perkins, ACS Nano 13, 4220-4229 (2019).
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Patrick Heenan, Thomas Perkins, ACS Nano 13, 4220-4229 (2019).
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Quantifying the initial unfolding of bacteriorhodopsin reveals retinal stabilization
Hao Yu, Patrick Heenan, Devin Edwards, Lyle Uyetake, Thomas Perkins, Angewandte Chemie 131, 1724-1727 (2019).
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Hao Yu, Patrick Heenan, Devin Edwards, Lyle Uyetake, Thomas Perkins, Angewandte Chemie 131, 1724-1727 (2019).
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2018
High-precision single-molecule characterization of the folding of an HIV RNA hairpin by atomic force microscopy
Robert Walder, William Van Patten, Dustin Ritchie, Rebecca Montange, Ty Miller, Michael Woodside, Thomas Perkins, Nano Letters 18, 6318-6325 (2018).
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Robert Walder, William Van Patten, Dustin Ritchie, Rebecca Montange, Ty Miller, Michael Woodside, Thomas Perkins, Nano Letters 18, 6318-6325 (2018).
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FEATHER: Automated Analysis of Force Spectroscopy Unbinding and Unfolding Data via a Bayesian Algorithm
Patrick Heenan, Thomas Perkins, Biophysical Journal 115, 757-762 (2018).
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Patrick Heenan, Thomas Perkins, Biophysical Journal 115, 757-762 (2018).
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Going vertical to improve accuracy in AFM-based single-molecule force spectroscopy
Robert Walder, William Van Patten, Ayush Adhikari, Thomas Perkins, ACS Nano 12, 198-207 (2018).
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Robert Walder, William Van Patten, Ayush Adhikari, Thomas Perkins, ACS Nano 12, 198-207 (2018).
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Improved free-energy landscape quantification illustrated with a computationally designed protein-ligand interaction
William Van Patten, Robert Walder, Ayush Adhikari, Stephen Okoniewski, Rashmi Ravichandran, Christine Tinberg, David Baker, Thomas Perkins, ChemPhysChem 19, 19-23 (2018).
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William Van Patten, Robert Walder, Ayush Adhikari, Stephen Okoniewski, Rashmi Ravichandran, Christine Tinberg, David Baker, Thomas Perkins, ChemPhysChem 19, 19-23 (2018).
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Improved free-energy landscape reconstruction of bacteriorhodopsin highlights local variations in unfolding energy
Patrick Heenan, Hao Yu, Matthew Siewny, Thomas Perkins, The Journal of Chemical Physics 148, 123313 (2018).
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Patrick Heenan, Hao Yu, Matthew Siewny, Thomas Perkins, The Journal of Chemical Physics 148, 123313 (2018).
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2017
Force spectroscopy with 9-μs resolution and sub-pN stability by tailoring AFM cantilever geometry
Devin Edwards, Jaevyn Faulk, Marc-Andre LeBlanc, Thomas Perkins, Biophysical Journal 113, 2595-2600 (2017).
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Devin Edwards, Jaevyn Faulk, Marc-Andre LeBlanc, Thomas Perkins, Biophysical Journal 113, 2595-2600 (2017).
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Force-activated DNA substrates for probing individual proteins interacting with single-stranded DNA
Stephen Okoniewski, Lyle Uyetake, Thomas Perkins, Nucleic Acids Research 45, 10775-10782 (2017).
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Stephen Okoniewski, Lyle Uyetake, Thomas Perkins, Nucleic Acids Research 45, 10775-10782 (2017).
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Rapid characterization of a mechanically labile α-helical protein enabled by efficient site-specific bioconjugation
Robert Walder, Marc-Andre LeBlanc, William Van Patten, Devin Edwards, Jacob Greenberg, Ayush Adhikari, Stephen Okoniewski, Ruby Sullan, David Rabuka, Marcelo Sousa, Thomas Perkins, Journal of the American Chemical Society 139, 9867-9875 (2017).
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Robert Walder, Marc-Andre LeBlanc, William Van Patten, Devin Edwards, Jacob Greenberg, Ayush Adhikari, Stephen Okoniewski, Ruby Sullan, David Rabuka, Marcelo Sousa, Thomas Perkins, Journal of the American Chemical Society 139, 9867-9875 (2017).
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Hidden dynamics in the unfolding of individual bacteriorhodopsin proteins
Hao Yu, Matthew Siewny, Devin Edwards, Aric Sanders, Thomas Perkins, Science 355, 945-950 (2017).
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Hao Yu, Matthew Siewny, Devin Edwards, Aric Sanders, Thomas Perkins, Science 355, 945-950 (2017).
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A surface-coupled optical trap with 1-bp precision via active stabilization
Stephen Okoniewski, Ashley Carter, Thomas Perkins, Methods in Molecular Biology 1486, 77-107 (2017).
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Stephen Okoniewski, Ashley Carter, Thomas Perkins, Methods in Molecular Biology 1486, 77-107 (2017).
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Improved force spectroscopy using focused-ion-beam modified cantilevers
Jaevyn Faulk, Devin Edwards, Matthew Bull, Thomas Perkins, Methods in Enzymology 582, 321-351 (2017).
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Jaevyn Faulk, Devin Edwards, Matthew Bull, Thomas Perkins, Methods in Enzymology 582, 321-351 (2017).
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Optimizing force spectroscopy by modifying commercial cantilevers: Improved stability, precision, and temporal resolution
Devin Edwards, Thomas Perkins, Journal of Structural Biology 197, 13-25 (2017).
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Devin Edwards, Thomas Perkins, Journal of Structural Biology 197, 13-25 (2017).
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2016
Sequence-dependent nanometer-scale conformational dynamics of individual RecBCD-DNA complexes
Ashley Carter, Maasa Seaberg, Hsiu-Fang Fan, Gang Sun, Christopher Wilds, Hung-Wen Li, Thomas Perkins, Nucleic Acids Research 44, 5849-5860 (2016).
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Ashley Carter, Maasa Seaberg, Hsiu-Fang Fan, Gang Sun, Christopher Wilds, Hung-Wen Li, Thomas Perkins, Nucleic Acids Research 44, 5849-5860 (2016).
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2015
Optimizing 1-μs-resolution single-molecule force spectroscopy on a commercial AFM
Devin Edwards, Jaevyn Faulk, Aric Sanders, Matthew Bull, Robert Walder, Marc-Andre LeBlanc, Marcelo Sousa, Thomas Perkins, Nano Letters , 151005120507003 (2015).
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Devin Edwards, Jaevyn Faulk, Aric Sanders, Matthew Bull, Robert Walder, Marc-Andre LeBlanc, Marcelo Sousa, Thomas Perkins, Nano Letters , 151005120507003 (2015).
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Direct observation of the reversible two-state unfolding and refolding of an α/β protein by single-molecule atomic force microscopy
Chengzhi He, Chunguang Hu, Xiaodong Hu, Xiaotang Hu, Adam Xiao, Thomas Perkins, Hongbin Li, Angewandte Chemie International Edition 54, 9921-9925 (2015).
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Chengzhi He, Chunguang Hu, Xiaodong Hu, Xiaotang Hu, Adam Xiao, Thomas Perkins, Hongbin Li, Angewandte Chemie International Edition 54, 9921-9925 (2015).
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Ultrastable measurement platform: sub-nm drift over hours in 3D at room temperature
Robert Walder, Hern Paik, Matthew Bull, Carl Sauer, Thomas Perkins, Optics Express 23, 16554 (2015).
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Robert Walder, Hern Paik, Matthew Bull, Carl Sauer, Thomas Perkins, Optics Express 23, 16554 (2015).
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2014
Ångström-precision optical traps and applications
Thomas Perkins, Annual Review of Biophysics 43, 279-302 (2014).
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Thomas Perkins, Annual Review of Biophysics 43, 279-302 (2014).
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Ultrastable atomic force microscopy: Improved force and positional stability
A. Churnside, Thomas Perkins, FEBS Letters 588, 3621-3630 (2014).
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A. Churnside, Thomas Perkins, FEBS Letters 588, 3621-3630 (2014).
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Improved single-molecule force spectroscopy using micromachined cantilevers
Matthew Bull, Ruby Sullan, Hongbin Li, Thomas Perkins, ACS Nano 8, 4984-4995 (2014).
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Matthew Bull, Ruby Sullan, Hongbin Li, Thomas Perkins, ACS Nano 8, 4984-4995 (2014).
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2013
Nano-chemical infrared imaging of membrane proteins in lipid bilayers
Samuel Berweger, D. Nguyen, Eric Muller, Hans Bechtel, Thomas Perkins, Markus Raschke, Journal of the American Chemical Society 135, 18292-18295 (2013).
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Samuel Berweger, D. Nguyen, Eric Muller, Hans Bechtel, Thomas Perkins, Markus Raschke, Journal of the American Chemical Society 135, 18292-18295 (2013).
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Torsionally constrained DNA for single-molecule assays: an efficient, ligation-free method
Hern Paik, V. Roskens, Thomas Perkins, Nucleic Acids Research 41, e179 - e179 (2013).
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Hern Paik, V. Roskens, Thomas Perkins, Nucleic Acids Research 41, e179 - e179 (2013).
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Atomic force microscopy with sub-picoNewton force stability for biological applications
Ruby Sullan, A. Churnside, D. Nguyen, Matthew Bull, Thomas Perkins, Methods 60, 131-141 (2013).
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Ruby Sullan, A. Churnside, D. Nguyen, Matthew Bull, Thomas Perkins, Methods 60, 131-141 (2013).
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Optimizing bead size reduces errors in force measurements in optical traps
Rebecca Montange, Matthew Bull, Elisabeth Shanblatt, Thomas Perkins, Optics Express 21, 39 (2013).
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Rebecca Montange, Matthew Bull, Elisabeth Shanblatt, Thomas Perkins, Optics Express 21, 39 (2013).
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2012
Dynamics and multiple stable binding modes of DNA intercalators revealed by single molecule force spectroscopy
Hern Paik, Thomas Perkins, Angewandte Chemie International Edition 51, 1731-1731 (2012).
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Hern Paik, Thomas Perkins, Angewandte Chemie International Edition 51, 1731-1731 (2012).
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Routine and timely sub-picoNewton force stability and precision for biological applications of atomic force microscopy
A. Churnside, Ruby Sullan, D. Nguyen, Sara Case, Matthew Bull, G. King, Thomas Perkins, Nano Letters 12, 3557-3561 (2012).
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A. Churnside, Ruby Sullan, D. Nguyen, Sara Case, Matthew Bull, G. King, Thomas Perkins, Nano Letters 12, 3557-3561 (2012).
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Single-molecule optical-trapping measurements with DNA anchored to an array of gold nanoposts
Hern Paik, Thomas Perkins, Methods in Molecular Biology 875, 335-356 (2012).
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Hern Paik, Thomas Perkins, Methods in Molecular Biology 875, 335-356 (2012).
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2011
Overstretching DNA at 65 pN does not require peeling from free ends or nicks
Hern Paik, Thomas Perkins, Journal of the American Chemical Society 133, 3219-3221 (2011).
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Hern Paik, Thomas Perkins, Journal of the American Chemical Society 133, 3219-3221 (2011).
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2010
Label-free optical imaging of membrane patches for atomic force microscopy
A. Churnside, G. King, Thomas Perkins, Optics Express 18, 23924 (2010).
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A. Churnside, G. King, Thomas Perkins, Optics Express 18, 23924 (2010).
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2009
Single-molecule studies of RecBCD
Thomas Perkins, Hung-Wen Li, Methods in Molecular Biology 587, 155-172 (2009).
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Thomas Perkins, Hung-Wen Li, Methods in Molecular Biology 587, 155-172 (2009).
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Integrating a high-force optical trap with gold nanoposts and a robust gold-DNA bond
Hern Paik, Y. Seol, W. Halsey, Thomas Perkins, Nano Letters 9, 2978-2983 (2009).
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Hern Paik, Y. Seol, W. Halsey, Thomas Perkins, Nano Letters 9, 2978-2983 (2009).
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Precision surface-coupled optical-trapping assay with 1 base-pair resolution
Ashley Carter, Yeonee Seol, Thomas Perkins, Biophysical Journal 96, 2926-2934 (2009).
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Ashley Carter, Yeonee Seol, Thomas Perkins, Biophysical Journal 96, 2926-2934 (2009).
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Ultrastable atomic force microscopy: atomic-scale stability and registration in ambient conditions
G. King, A. Carter, A. Churnside, L. Eberle, Thomas Perkins, Nano Letters 9, 1451-1456 (2009).
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G. King, A. Carter, A. Churnside, L. Eberle, Thomas Perkins, Nano Letters 9, 1451-1456 (2009).
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Optical traps for single molecule biophysics: a primer
Thomas Perkins, Laser & Photonics Review 3, 203-220 (2009).
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Thomas Perkins, Laser & Photonics Review 3, 203-220 (2009).
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2007
Elasticity of short DNA molecules: theory and experiment for contour lengths of 0.6–7 μm
Yeonee Seol, Jinyu Li, Philip Nelson, Thomas Perkins, M. Betterton, Biophysical Journal 93, 4360-4373 (2007).
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Yeonee Seol, Jinyu Li, Philip Nelson, Thomas Perkins, M. Betterton, Biophysical Journal 93, 4360-4373 (2007).
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Back-scattered detection provides atomic-scale localization precision, stability, and registration in 3D
A. Carter, G. King, Thomas Perkins, Optics Express 15, 13434 (2007).
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A. Carter, G. King, Thomas Perkins, Optics Express 15, 13434 (2007).
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TFIIA changes the conformation of the DNA in TBP/TATA complexes and increases their kinetic stability
A. Hieb, W. Halsey, M. Betterton, Thomas Perkins, Jennifer Kugel, James Goodrich, Journal of Molecular Biology 372, 619-632 (2007).
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A. Hieb, W. Halsey, M. Betterton, Thomas Perkins, Jennifer Kugel, James Goodrich, Journal of Molecular Biology 372, 619-632 (2007).
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Stabilization of an optical microscope to 0.1 nm in three dimensions
A. Carter, G. King, T. Ulrich, W. Halsey, David Alchenberger, Thomas Perkins, Applied Optics 46, 421 (2007).
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A. Carter, G. King, T. Ulrich, W. Halsey, David Alchenberger, Thomas Perkins, Applied Optics 46, 421 (2007).
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2006
Gold nanoparticles: enhanced optical trapping and sensitivity coupled with significant heating
Y. Seol, A. Carpenter, Thomas Perkins, Optics Letters 31, 2429 (2006).
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Y. Seol, A. Carpenter, Thomas Perkins, Optics Letters 31, 2429 (2006).
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2004
Measuring 0.1-nm motion in 1 ms in an optical microscope with differential back-focal-plane detection
L. Nugent-Glandorf, Thomas Perkins, Optics Letters 29, 2611 (2004).
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L. Nugent-Glandorf, Thomas Perkins, Optics Letters 29, 2611 (2004).
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Forward and reverse motion of single RecBCD molecules on DNA
Thomas Perkins, Hung-Wen Li, Ravindra Dalal, Jeff Gelles, Steven Block, Biophysical Journal 86, 1640-1648 (2004).
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Thomas Perkins, Hung-Wen Li, Ravindra Dalal, Jeff Gelles, Steven Block, Biophysical Journal 86, 1640-1648 (2004).
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2003
Sequence-dependent pausing of single lambda exonuclease molecules
Thomas Perkins, Ravindra Dalal, Paul Mitsis, Steven Block, Science 301, 1914-1918 (2003).
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Thomas Perkins, Ravindra Dalal, Paul Mitsis, Steven Block, Science 301, 1914-1918 (2003).
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1999
Single polymers in elongational flows: dynamic, steady-state, and population-averaged properties
Thomas Perkins, D. Smith, S. Chu, Flexible Polymer Chains in Elongational Flow , 283-334 (1999).
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Thomas Perkins, D. Smith, S. Chu, Flexible Polymer Chains in Elongational Flow , 283-334 (1999).
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The hydrodynamics of a DNA molecule in a flow field
R. Larson, Thomas Perkins, D. Smith, S. Chu, Flexible Polymer Chains in Elongational Flow , 259-282 (1999).
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R. Larson, Thomas Perkins, D. Smith, S. Chu, Flexible Polymer Chains in Elongational Flow , 259-282 (1999).
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1997
Single polymer dynamics in an elongational flow
Thomas Perkins, Douglas Smith, Steven Chu, Science 276, 2016-2021 (1997).
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Thomas Perkins, Douglas Smith, Steven Chu, Science 276, 2016-2021 (1997).
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Hydrodynamics of a DNA molecule in a flow field
R. Larson, Thomas Perkins, D. Smith, S. Chu, Physical Review E 55, 1794-1797 (1997).
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R. Larson, Thomas Perkins, D. Smith, S. Chu, Physical Review E 55, 1794-1797 (1997).
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1996
Dynamical scaling of DNA diffusion coefficients
Douglas Smith, Thomas Perkins, Steven Chu, Macromolecules 29, 1372-1373 (1996).
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Douglas Smith, Thomas Perkins, Steven Chu, Macromolecules 29, 1372-1373 (1996).
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1995
Self-diffusion of an entangled DNA molecule by reptation
Douglas Smith, Thomas Perkins, Steven Chu, Physical Review Letters 75, 4146-4149 (1995).
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Douglas Smith, Thomas Perkins, Steven Chu, Physical Review Letters 75, 4146-4149 (1995).
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Stretching of a single tethered polymer in a uniform flow
Thomas Perkins, Douglas Smith, Ronald Larson, Steven Chu, Science 268, 83-87 (1995).
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Thomas Perkins, Douglas Smith, Ronald Larson, Steven Chu, Science 268, 83-87 (1995).
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1994
Direct observation of tube-like motion of a single polymer chain
Thomas Perkins, Douglas Smith, Steven Chu, Science 264, 819-822 (1994).
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Thomas Perkins, Douglas Smith, Steven Chu, Science 264, 819-822 (1994).
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Relaxation of a single DNA molecule observed by optical microscopy
Thomas Perkins, Stephen Quake, Douglas Smith, Steven Chu, Science 264, 822-826 (1994).
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Thomas Perkins, Stephen Quake, Douglas Smith, Steven Chu, Science 264, 822-826 (1994).
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1993
Steady‐state gain and saturation flux measurements in a high efficiency, electron‐beam‐pumped, Ar‐Xe laser
Thomas Perkins, Journal of Applied Physics 74, 4860-4866 (1993).
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Thomas Perkins, Journal of Applied Physics 74, 4860-4866 (1993).
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