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Applied Optics

Applied Optics


  • Vol. 37, Iss. 12 — Apr. 20, 1998
  • pp: 2315–2326

Monte Carlo Simulation of a Single-Molecule Detection Experiment

Dennis H. Bunfield and Lloyd M. Davis  »View Author Affiliations

Applied Optics, Vol. 37, Issue 12, pp. 2315-2326 (1998)

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The physical and instrumental processes that occur in experiments for the detection of individual fluorescent molecules in solution are described, with emphasis on their incorporation into a quantitative Monte Carlo simulation. The simulation is applied to the conditions of a past experiment [Appl. Opt. 34, 3208 (1995)], which utilizes a sheath flow system for high detection efficiency, and it generates comparable results, while helping to identify experimental limitations. The simulation indicates that the use of low dead-time electronics and appropriate selection of experimental parameters should enable detection at more rapid rates for applications in which large numbers of molecules are to be efficiently counted.

© 1998 Optical Society of America

OCIS Codes
(040.1880) Detectors : Detection
(120.0120) Instrumentation, measurement, and metrology : Instrumentation, measurement, and metrology
(170.6280) Medical optics and biotechnology : Spectroscopy, fluorescence and luminescence
(300.2530) Spectroscopy : Fluorescence, laser-induced

Dennis H. Bunfield and Lloyd M. Davis, "Monte Carlo Simulation of a Single-Molecule Detection Experiment," Appl. Opt. 37, 2315-2326 (1998)

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  1. L. Q. Li and L. M. Davis, “Rapid and efficient detection of single chromophore molecules in aqueous solution,” Appl. Opt. 34, 3208–3217 (1995), and references cited therein.
  2. E. B. Shera, N. K. Seitzinger, L. M. Davis, R. A. Keller, and S. A. Soper, “Detection of single fluorescent molecules,” Chem. Phys. Lett. 174, 553–557 (1990).
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  4. S. Nie and S. R. Emory, “Probing single nanoparticles by surface enhanced Raman scattering,” Science 275, 1102–1106 (1997).
  5. L. Q. Li and L. M. Davis, “Single photon avalanche diode for single molecule detection,” Rev. Sci. Instrum. 64, 1524–1529 (1993).
  6. S. A. Soper, Q. L. Mattingly, and P. Vegunta, “Photon burst detection of single near-infrared fluorescent molecules,” Anal. Chem. 65, 740–747 (1993).
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  12. P. M. Goodwin, R. L. Affleck, W. P. Ambrose, J. H. Jett, M. E. Johnson, J. C. Martin, J. T. Petty, J. A. Schecker, M. Wu, and R. A. Keller, “Detection of single fluorescent molecules in flowing sample streams,” in Computer Assisted Analytical Spectroscopy, S. D. Brown, ed. (Wiley, Sussex, England, 1996), pp. 61–80.
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  14. L. M. Davis and L. Q. Li, “Monte Carlo model of a single molecule counting experiment,” in Laser Applications to Chemical Analysis, Vol. 5 of 1994 OSA Technical Digest Series (Optical Society of America, Washington, D.C., 1994), pp. 206–209.
  15. R. A. Mathies, K. Peck, and L. Stryer, “Optimization of high-sensitivity fluorescence detection,” Anal. Chem. 62, 1786–1791 (1990).
  16. L. M. Davis, L. Q. Li, E. B. Shera, A. Castro, and S. A. Soper, “Photon statistics for the detection of single molecules in solution,” in Quantum Electronics and Laser Science, Vol. 13 of OSA Technical Digest Series (Optical Society of America (Washington, D.C., 1992), pp. 70–72.
  17. S. A. Soper, L. M. Davis, and E. B. Shera, “Detection and identification of single molecules in solution,” J. Opt. Soc. Am. B 9, 1761–1769 (1992).
  18. C. Zander, M. Sauer, K. H. Drexage, D. S. Ko, A. Schultz, J. Wolfrum, L. Brand, C. Eggeling, and C. A. M. Seidel, “Detection and characterization of single molecules in aqueous solution,” Appl. Phys. B 63, 517–523 (1996).
  19. D. H. Bunfield, “Simulation of a single molecule detection experiment,” M.S. thesis (University of Tennessee, Knoxville, Tennessee, 1997).
  20. L. M. Davis and D. H. Bunfield, “Spectroscopic identification of individually detected fluorescent molecules,” The Fifth International Conference on Methods and Applications of Fluorescence Spectroscopy, Berlin, 1997. Book of Abstracts, W. Rettig, ed. (Springer-Verlag, Berlin, 1997), p. 27.
  21. A. Spinelli, L. M. Davis, and H. Dautet, “Actively quenched single-photon avalanche diode for high repetition rate time-gated photon counting,” Rev. Sci. Instrum. 67, 55–61 (1996).
  22. J. C. Fister III, S. C. Jacobson, L. M. Davis, and J. M. Ramsey, “Counting single-chromophore molecules for ultrasensitive analysis and separations on microchip devices,” Anal. Chem. 70, 431–437 (1997).
  23. One significant application currently under development that demands efficient and unambiguous SMD is rapid DNA sequencing. Also, efficient processing of the sample is desirable for assay of miniscule sample quantities, such as the components of a single cell and genetic screening without DNA amplification by polymerase chain reaction. See references of Ref. 1.
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  26. H. Qian and E. L. Elson, “Analysis of confocal laser-induced microscope optics for 3-D fluorescence correlation spectroscopy,” Appl. Opt. 30, 1185–1195 (1991).
  27. S. A. Soper, H. L. Nutter, R. A. Keller, L. M. Davis, and E. B. Shera, “The photophysical constants of several fluorescent dyes pertaining to ultrasensitive fluorescence spectroscopy,” Photochem. Photobiol. 57, 972–977 (1993).
  28. L. M. Davis, L. E. Schneider, and D. B. Bunfield, “Increasing the rate of detection of single molecules in solution,” in Laser Applications to Chemical, Biological, and Environmental Analysis, Vol. 3 of 1996 OSA Technical Digest Series (Optical Society of America, Washington, D.C., 1996), pp. 24–26.
  29. L. M. Davis, “Efficient counting of single molecules with sub-100 μs transit times,” paper BC.06 at American Physical Society SES97 meeting, Nashville, November 1997, http://aps.org/BAPSSES97/abs/S700006.html/.
  30. J. Widengren, R. Rigler, and U. Mets, “Triplet-state monitoring by fluorescence correlation spectroscopy,” J. Fluorescence 4, 255–258 (1994).

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