Length: Barely 13 pages (Optics Express typically runs between 5-18 pages)

Partial list of changes and known issues

Science

• SIMPLIFIED: Text uses simple Gaussian ellipsoid model of diffraction-limited observation profile, with small footnote regarding corrections for non-Gaussianity
• FIXED: Misplaced long-pass filter in diffraction-limited FCS figure
• ADDED: Peclet number in discussion of the zero-crossing of the diffraction-limited FCS signal
• ADDED: Error bars on dimensions of ZMWs based on SEMs
• FIXED: Typographical error in Eqns. for kinetic rate uncertainty
• ADDED: Peclet number in discussion of diffusive broadening and kinetic rate uncertainty

English

• REPLACED: New title is both a complete sentence and accurate
• REVISED: More quantitative and analytical results in abstract
• REPLACED: Introduction: Motivation in terms of mixers and brief discussion of FCS/ZMW replaces overview of single-molecule detection
• ADDED: Outline of logic and organization of paper now presented early in introduction
• REVISED: Clarified that our experiment cannot be expected to satisfy the assumptions originally used in deriving the ZMW fitting function we use

Formatting

• IMPROVED: Plot readability using thicker lines and high-contrast, easily-identified colors, larger font, legend

Known issues

[Some known issues are marked in the paper directly in footnotes labeled "Do not submit"]

• Truncation/laser intensity sentence has not been corrected: the SNR results are not affected meaningfully by including correlation data in fits. I would still like to include the truncation to make the paper mimic data analysis I expect a researcher to do by intuition (restrict fit to the region where the function does something)--need to cite examples
• Offset not accounted-for in correlation data for zero-mode waveguides
• Absolute concentration for diffraction-limited data poorly constrained: must review earlier correlation curves from known concentrations in the Eurotrash FCS (A footnote is included in the paper)
• Phenomenology of gold transparency at 488 nm not addressed
• Citations not updated uniformly since previous discussion
• Broken summary
• Language has not been condensed or stylized for readability
• Optics Express language style guide not yet applied

ReactionFCS2OE.pdf Compiled PDF

Riehn200710.pdf Robert Riehn's notes on this version of the paper

ReactionFCS2OE.20071025.zip LaTeX source formatted with Optics Express template

FCSDataDirectory.zip Complete raw data from diffraction-limited and zero-mode waveguide experiments. The diffraction limited correlation curves measured away from the channel surface are in folder FCS Data TruncatedNOSURFACE (which contains a subset of measurements from the summer of 2006 in folder FCS Data 20060802). The zero mode waveguide from 2006 summer are in NanopitsRAW20060807. The MATLAB commands that run the analysis and makes plots of these data are first SingleLobe = [1.0 0.3e-6 0.3e-6 6e-6 0 0 0]; and then [v N LCGConcentrations] = FCSStatistics2006SplineLCGandZMWOEColor('NanopitsRAW20060807',2e-6,0.2,190e-6,0.0055,'FCS Data TruncatedNOSURFACE',120e-6,0.0056,2e-5,0.9975,5.14e-12,1.1,SingleLobe);