SMART – Analyzing single molecule data

Max Greenfeld, Dmitri S. Pavlichin, Hideo Mabuchi and Daniel Herschlag, “Single Molecule Analysis Research Tool (SMART): An Integrated Approach for Analyzing Single Molecule Data,” PLoS ONE 7(2): e30024. doi:10.1371/journal.pone.0030024…

Intramolecular FCS in a feedback tracking microscope

Kevin McHale and Hideo Mabuchi, “Intramolecular fluorescence correlation spectroscopy in a feedback tracking microscope,” Biophys. J. 99, 313-322, (2010). arXiv:0908.1177
online…

Precise characterization of conformation fluctuations of DNA

Kevin McHale and Hideo Mabuchi, “Precise characterization of the conformation fluctuations of freely diffusing DNA: beyond Rouse and Zimm,” J. Am. Chem. Soc. 131, 17901-17907, (2009); e-print (no subscription required). online additional info…

Quantum dot photon statistics by particle tracking

Kevin McHale, Andrew J. Berglund and Hideo Mabuchi, “Quantum dot photon statistics measured by three-dimensional particle tracking,” Nano Letters 7, 3535-3539, (2007); e-print (no subscription needed); featured in the Jan. 2008 issue of Photonics Spectra. online…

Fluctuations in closed-loop particle tracking

Andrew J. Berglund, Kevin McHale, and Hideo Mabuchi, “Fluctuations in closed-loop fluorescent particle tracking,” Opt. Express 15, 7752-7773, (2007). PDF online…

Cavity-enhanced spectroscopy of biomolecules in solution

Tim McGarvey, Andre Conjusteau and Hideo Mabuchi, “Finesse and sensitivity gain in cavity-enhanced absorption spectroscopy of biomolecules in solution,” Optics Express 14, 10441-10451, (2006). PDF online…

Feedback localization near the shot-noise limit

Andrew J. Berglund, Kevin McHale and Hideo Mabuchi, “Feedback localization of freely diffusing fluorescent particles near the optical shot-noise limit,” Opt. Lett. 32, 145-147, (2007). PDF online…

Kevin McHale’s Ph.D. thesis

Kevin L. McHale, “Feedback tracking and correlation spectroscopy of fluorescent nanoparticles and biomolecules.” Ph.D. thesis, defended 1/8/08. online…

Performance bounds on single-particle tracking

Andrew J. Berglund and Hideo Mabuchi, “Performance bounds on single-particle tracking by fluorescence modulation,” Appl. Phys. B 83, 127-133, (2006). PDF online…

Tracking-FCS

Andrew J. Berglund and Hideo Mabuchi, “Tracking-FCS: Fluorescence correlation spectroscopy of individual particles,” Opt. Express 13, 8069-8082, (2005). PDF online…

Nonexponential statistics of photobleaching

Andrew J. Berglund, “Nonexponential statistics of fluorescence photobleaching,” J. Chem. Phys. 121, 2899, (2004). PDF online…

Andrew Berglund’s Ph.D. thesis

Andrew J. Berglund, “Feedback Control of Brownian Motion for Single-Particle Fluorescence Spectroscopy.” Ph.D. thesis, defended 9/27/06. online…

Bayesian estimation for single-molecule identification

Kevin McHale, Andrew J. Berglund, and Hideo Mabuchi, “Bayesian estimation for species identification in single-molecule fluorescence microscopy,” Biophys. J. 86, 3409, (2004). PDF online…

Feedback controller design for tracking

Andrew J. Berglund and Hideo Mabuchi, “Feedback controller design for tracking a single fluorescent molecule,” Appl. Phys. B 78, 653, (2004). PDF online…

Photon statistics and dynamics of FRET

A. J. Berglund, A. C. Doherty, and H. Mabuchi, “Photon statistics and dynamics of Fluorescence Resonance Energy Transfer,” Phys. Rev. Lett. 89, 068101, (2002). PDF cond-mat/0206031 online…