Thomas Perkins - Publications

University of Colorado / JILA, Boulder, CO, United States 
Single Molecule Biophysics

54 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Walder R, Van Patten WJ, Ritchie DB, Montange RK, Miller TW, Woodside MT, Perkins TT. High-Precision Single-Molecule Characterization of the Folding of an HIV RNA Hairpin by Atomic Force Microscopy. Nano Letters. PMID 30234311 DOI: 10.1021/acs.nanolett.8b02597  0.4
2017 Walder R, Van Patten WJ, Adhikari A, Perkins TT. Going Vertical to Improve the Accuracy of Atomic Force Microscopy Based Single-Molecule Force Spectroscopy. Acs Nano. PMID 29244486 DOI: 10.1021/acsnano.7b05721  0.36
2017 Van Patten WJ, Walder R, Adhikari A, Okoniewski SR, Ravichandran R, Tinberg CE, Baker D, Perkins TT. Improved Free-Energy Landscape Quantification Illustrated with a Computationally Designed Protein-Ligand Interaction. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. PMID 29069529 DOI: 10.1002/cphc.201701147  0.76
2017 Okoniewski SR, Uyetake L, Perkins TT. Force-activated DNA substrates for probing individual proteins interacting with single-stranded DNA. Nucleic Acids Research. PMID 28977580 DOI: 10.1093/nar/gkx761  0.76
2017 Walder R, LeBlanc MA, Van Patten WJ, Edwards D, Greenberg JA, Adhikari A, Okoniewski SR, Sullan RMA, Rabuka D, Sousa MC, Perkins TT. Rapid Characterization of a Mechanically Labile α-helical Protein Enabled by Efficient Site-Specific Bioconjugation. Journal of the American Chemical Society. PMID 28677396 DOI: 10.1021/jacs.7b02958  0.76
2017 Faulk JK, Edwards DT, Bull MS, Perkins TT. Improved Force Spectroscopy Using Focused-Ion-Beam-Modified Cantilevers. Methods in Enzymology. 582: 321-351. PMID 28062041 DOI: 10.1016/bs.mie.2016.08.007  0.44
2017 Okoniewski SR, Carter AR, Perkins TT. A Surface-Coupled Optical Trap with 1-bp Precision via Active Stabilization. Methods in Molecular Biology (Clifton, N.J.). 1486: 77-107. PMID 27844426 DOI: 10.1007/978-1-4939-6421-5_4  1
2016 Carter AR, Seaberg MH, Fan HF, Sun G, Wilds CJ, Li HW, Perkins TT. Sequence-dependent nanometer-scale conformational dynamics of individual RecBCD-DNA complexes. Nucleic Acids Research. PMID 27220465 DOI: 10.1093/nar/gkw445  1
2016 Edwards DT, Perkins TT. Optimizing force spectroscopy by modifying commercial cantilevers: improved stability, precision, and temporal resolution. Journal of Structural Biology. PMID 26804584 DOI: 10.1016/j.jsb.2016.01.009  1
2015 Edwards DT, Faulk JK, Sanders AW, Bull MS, Walder R, LeBlanc MA, Sousa MC, Perkins TT. Optimizing 1-μs-Resolution Single-Molecule Force Spectroscopy on a Commercial Atomic Force Microscope. Nano Letters. 15: 7091-8. PMID 26421945 DOI: 10.1021/acs.nanolett.5b03166  1
2015 Walder R, Paik DH, Bull MS, Sauer C, Perkins TT. Ultrastable measurement platform: sub-nm drift over hours in 3D at room temperature. Optics Express. 23: 16554-64. PMID 26191667 DOI: 10.1364/OE.23.016554  1
2014 Churnside AB, Perkins TT. Ultrastable atomic force microscopy: improved force and positional stability. Febs Letters. 588: 3621-30. PMID 24801176 DOI: 10.1016/j.febslet.2014.04.033  1
2014 Perkins TT. Ångström-precision optical traps and applications. Annual Review of Biophysics. 43: 279-302. PMID 24773015 DOI: 10.1146/annurev-biophys-042910-155223  1
2014 Bull MS, Sullan RM, Li H, Perkins TT. Improved single molecule force spectroscopy using micromachined cantilevers. Acs Nano. 8: 4984-95. PMID 24670198 DOI: 10.1021/nn5010588  1
2013 Berweger S, Nguyen DM, Muller EA, Bechtel HA, Perkins TT, Raschke MB. Nano-chemical infrared imaging of membrane proteins in lipid bilayers. Journal of the American Chemical Society. 135: 18292-5. PMID 24251914 DOI: 10.1021/ja409815g  1
2013 Paik DH, Roskens VA, Perkins TT. Torsionally constrained DNA for single-molecule assays: an efficient, ligation-free method. Nucleic Acids Research. 41: e179. PMID 23935118 DOI: 10.1093/nar/gkt699  1
2013 Sullan RM, Churnside AB, Nguyen DM, Bull MS, Perkins TT. Atomic force microscopy with sub-picoNewton force stability for biological applications. Methods (San Diego, Calif.). 60: 131-41. PMID 23562681 DOI: 10.1016/j.ymeth.2013.03.029  1
2013 Montange RK, Bull MS, Shanblatt ER, Perkins TT. Optimizing bead size reduces errors in force measurements in optical traps. Optics Express. 21: 39-48. PMID 23388894 DOI: 10.1364/OE.21.000039  1
2013 King GM, Churnside AB, Perkins TT. A precision force microscope for biophysics Conference Proceedings of the Society For Experimental Mechanics Series. 6: 31-36. DOI: 10.1007/978-1-4614-4436-7_5  1
2012 Churnside AB, Sullan RM, Nguyen DM, Case SO, Bull MS, King GM, Perkins TT. Routine and timely sub-picoNewton force stability and precision for biological applications of atomic force microscopy. Nano Letters. 12: 3557-61. PMID 22694769 DOI: 10.1021/nl301166w  1
2012 Paik DH, Perkins TT. Single-molecule optical-trapping measurements with DNA anchored to an array of gold nanoposts. Methods in Molecular Biology (Clifton, N.J.). 875: 335-56. PMID 22573450 DOI: 10.1007/978-1-61779-806-1_18  1
2012 Paik DH, Perkins TT. Dynamics and multiple stable binding modes of DNA intercalators revealed by single-molecule force spectroscopy. Angewandte Chemie (International Ed. in English). 51: 1811-5. PMID 22162006 DOI: 10.1002/anie.201105540  1
2012 Paik DH, Perkins TT. Force spectroscopy of DNA: There is still a lot to learn Proceedings of Spie - the International Society For Optical Engineering. 8458. DOI: 10.1117/12.945812  1
2011 Paik DH, Perkins TT. Overstretching DNA at 65 pN does not require peeling from free ends or nicks. Journal of the American Chemical Society. 133: 3219-21. PMID 21207940 DOI: 10.1021/ja108952v  1
2010 Churnside AB, King GM, Perkins TT. Label-free optical imaging of membrane patches for atomic force microscopy. Optics Express. 18: 23924-32. PMID 21164738 DOI: 10.1364/OE.18.023924  1
2010 Perkins TT, Li HW. Single-molecule studies of RecBCD. Methods in Molecular Biology (Clifton, N.J.). 587: 155-72. PMID 20225148 DOI: 10.1007/978-1-60327-355-8_11  1
2010 King GM, Churnside AB, Perkins TT. Optical trapping meets atomic force microscopy: A precision force microscope for biophysics Proceedings of Spie - the International Society For Optical Engineering. 7762. DOI: 10.1117/12.862745  1
2010 Perkins TT, Malley CV, Dubson M, Perkins KK. An interactive optical tweezers simulation for science education Proceedings of Spie - the International Society For Optical Engineering. 7762. DOI: 10.1117/12.862030  1
2010 Perkins TT, King GM, Churnside AB, Carter AR. Ultrastable atomic force microscopy using laser-based, active noise cancelation Optics Infobase Conference Papers 1
2010 Perkins TT, King GM, Churnside AB, Carter AR. Ultrastable atomic force microscopy using laser-based, active noise cancelation Optics Infobase Conference Papers 1
2009 Paik DH, Seol Y, Halsey WA, Perkins TT. Integrating a high-force optical trap with gold nanoposts and a robust gold-DNA bond. Nano Letters. 9: 2978-83. PMID 19492836 DOI: 10.1021/nl901404s  1
2009 King GM, Carter AR, Churnside AB, Eberle LS, Perkins TT. Ultrastable atomic force microscopy: atomic-scale stability and registration in ambient conditions. Nano Letters. 9: 1451-6. PMID 19351191 DOI: 10.1021/nl803298q  1
2009 Carter AR, Seol Y, Perkins TT. Precision surface-coupled optical-trapping assay with one-basepair resolution. Biophysical Journal. 96: 2926-34. PMID 19348774 DOI: 10.1016/j.bpj.2008.12.3933  1
2009 Churnside AB, King GM, Perkins TT. Independent measurements of force and position in atomic force microscopy Proceedings of Spie - the International Society For Optical Engineering. 7405. DOI: 10.1117/12.826567  1
2009 Perkins TT. Dynamics of DNA-based molecular motors measured with 1-bp resolution Cleo/Europe - Eqec 2009 - European Conference On Lasers and Electro-Optics and the European Quantum Electronics Conference. DOI: 10.1109/CLEOE-EQEC.2009.5191666  1
2009 Perkins TT. Optical traps for single molecule biophysics: A primer Laser and Photonics Reviews. 3: 203-220. DOI: 10.1002/lpor.200810014  1
2008 Churnside AB, King GM, Carter AR, Perkins TT. Improved performance of an ultrastable measurement platform using a field-programmable gate array for real-time deterministic control Proceedings of Spie - the International Society For Optical Engineering. 7042. DOI: 10.1117/12.795700  1
2007 Carter AR, King GM, Perkins TT. Back-scattered detection provides atomic-scale localization precision, stability, and registration in 3D. Optics Express. 15: 13434-45. PMID 19550612 DOI: 10.1364/OE.15.013434  1
2007 Seol Y, Li J, Nelson PC, Perkins TT, Betterton MD. Elasticity of short DNA molecules: theory and experiment for contour lengths of 0.6-7 microm. Biophysical Journal. 93: 4360-73. PMID 17766363 DOI: 10.1529/biophysj.107.112995  1
2007 Hieb AR, Halsey WA, Betterton MD, Perkins TT, Kugel JF, Goodrich JA. TFIIA changes the conformation of the DNA in TBP/TATA complexes and increases their kinetic stability. Journal of Molecular Biology. 372: 619-32. PMID 17681538 DOI: 10.1016/j.jmb.2007.06.061  1
2007 Carter AR, King GM, Ulrich TA, Halsey W, Alchenberger D, Perkins TT. Stabilization of an optical microscope to 0.1 nm in three dimensions. Applied Optics. 46: 421-7. PMID 17228390 DOI: 10.1364/AO.46.000421  1
2006 Seol Y, Carpenter AE, Perkins TT. Gold nanoparticles: enhanced optical trapping and sensitivity coupled with significant heating. Optics Letters. 31: 2429-31. PMID 16880845 DOI: 10.1364/OL.31.002429  1
2005 Carter AR, King GM, Ulrich TA, Halsey WA, Perkins TT. 3D stabilization of an optical microscope to 0.1 nm at 1 Hz using an array of nano-posts Optics Infobase Conference Papers 1
2004 Nugent-Glandorf L, Perkins TT. Measuring 0.1-nm motion in 1 ms in an optical microscope with differential back-focal-plane detection. Optics Letters. 29: 2611-3. PMID 15552661 DOI: 10.1364/OL.29.002611  1
2004 Perkins TT, Li HW, Dalal RV, Gelles J, Block SM. Forward and reverse motion of single RecBCD molecules on DNA. Biophysical Journal. 86: 1640-8. PMID 14990491 DOI: 10.1016/S0006-3495(04)74232-0  1
2003 Perkins TT, Dalal RV, Mitsis PG, Block SM. Sequence-dependent pausing of single lambda exonuclease molecules. Science (New York, N.Y.). 301: 1914-8. PMID 12947034 DOI: 10.1126/science.1088047  1
1999 Larson RG, Perkins TT, Smith DE, Chu S. Single-molecule hydrodynamics of tethered and released DNA molecules Acs Symposium Series. 736: 196-207.  1
1997 Perkins TT, Smith DE, Chu S. Single polymer dynamics in an elongational flow. Science (New York, N.Y.). 276: 2016-21. PMID 9197259 DOI: 10.1126/science.276.5321.2016  1
1997 Larson RG, Perkins TT, Smith DE, Chu S. Hydrodynamics of a DNA molecule in a flow field Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 55: 1794-1797.  1
1995 Smith DE, Perkins TT, Chu S. Self-diffusion of an entangled DNA molecule by reptation. Physical Review Letters. 75: 4146-4149. PMID 10059826 DOI: 10.1103/PhysRevLett.75.4146  1
1995 Perkins TT, Smith DE, Larson RG, Chu S. Stretching of a single tethered polymer in a uniform flow. Science (New York, N.Y.). 268: 83-7. PMID 7701345  1
1994 Perkins TT, Quake SR, Smith DE, Chu S. Relaxation of a single DNA molecule observed by optical microscopy. Science (New York, N.Y.). 264: 822-6. PMID 8171336  1
1994 Perkins TT, Smith DE, Chu S. Direct observation of tube-like motion of a single polymer chain. Science (New York, N.Y.). 264: 819-22. PMID 8171335  1
1993 Perkins TT. Steady-state gain and saturation flux measurements in a high efficiency, electron-beam-pumped, Ar-Xe laser Journal of Applied Physics. 74: 4860-4866. DOI: 10.1063/1.354315  1
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