Doug Smith Research Papers

Doug Smith – Research Papers

Web: http://physics.ucsd.edu/~des Email: des@physics.ucsd.edu
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41. Identification of a rapidly formed nonnucleosomal histone-DNA intermediate that is converted into chromatin by ACF

S.E. Torigoe, D.L. Urwin, H. Ishii, D.E. Smith, J.T. Kadonaga

Molecular Cell 43, 638 (2011) (PDF file)

40. Single-molecule studies of viral DNA packaging

D. E. Smith

Current Opinion in Virology 1, 134 (2011) (PDF file)

39. Single-molecule studies of viral DNA packaging

Y. Chemla, D. E. Smith

Book Chapter in Viral Molecular Machines, Edited by V. Rao and M. Rossmann, Springer (in press, 2011) (PDF file)

38. Mutations altering a structurally conserved Loop-helix-loop region of a viral packaging motor change DNA translocation velocity and processivity
J. M. Tsay, J. Sippy, D. del Toro, B. T. Andrews, B. Draper, V. Rao, C. Catalano, M. Feiss, D. E. Smith,

Journal of Biological Chemistry 285:24282 (2010) (PDF file)

37. Biophysics of Knotting, D. Meluzzi, D. E. Smith, G. Arya,

Annual Reviews of Biophysics 39, 349 (2010) (PDF file)

36. The Q motif of a viral packaging motor governs its force generation and communicates ATP recognition to DNA interaction
J. M. Tsay, J. Sippy, M. Feiss, D. E. Smith,
Proceedings of the National Academy of Sciences USA 104, 16868 (2009) (PDF file)

35. Portal motor velocity and internal force resisting viral DNA packaging in bacteriophage phi29
J. P. Rickgauer, D. Fuller, S. Grimes, P. Jardine, D. Anderson, D. E. Smith,
Biophysical Journal 94, 159 (2008) (PDF file) (supplemental data)

34. Single bacteriophage T4 DNA packaging motors exhibit large force generation, high velocity, and dynamic variability
      D. N. Fuller, D. M. Raymer, V. Kottadiel, V. B. Rao, and D. E. Smith,
Proceedings of the National Academy of Sciences USA 104, 16868 (2007) (PDF file)
       - News: PhysOrg, Science News Daily, UCSD

33. Measurements of single DNA molecule packaging dynamics in bacteriophage lambda reveal high forces, high motor processivity, and capsid transformations
      D. N. Fuller, D. Raymer, J. P. Rickgauer, R.M. Robertson, C. E. Catalano, D. L. Anderson, S. Grimes, D. E. Smith
      Journal of Molecular Biology, 373, 1113 (2007) (PDF file)
- Featured as the cover story of the Nov. 9 issue of Journal of Molecular Biology (cover image)

32. Direct measurement of the intermolecular forces confining a single molecule in an entangled polymer solution
      R. M. Robertson and D. E. Smith
      Physical Review Letters 99, 126001 (2007) (PDF file)
    - Highlighted in a commentary by R. Larson in Science: (commentary).

31. Direct measurement of the confining forces imposed on a single molecule in a concentrated solution of circular polymers
      R. M. Robertson and D. E. Smith
      Macromolecules, 40, 8737 (2007) (PDF file)

30. Spontaneous knotting of an agitated string
      D. M. Raymer and D. E. Smith,
      Proceedings of the National Academy of Sciences USA, 104, 16432 (2007) (link)
- #1 most read paper in PNAS, March 2009: http://www.pnas.org/content/104/42/16432.full
       - Highlighted in a commentary in PNAS by A. Belmonte (PDF file)
       - News articles in: San Diego Union Tribune (front page story), New York Times (named one of the “Top ideas of 2007”), Discover Magazine (2/08, p. 16), Popular Science,
Science News (long), Science News (short), Yahoo News (#1 most emailed news story on Dec. 4 & 5, front page story), Physics Today, New Scientist, AAAS Science Update,
Mathematical Assoc. of America News, Eureka Science, United Press International, La Presse, Null Hypothesis, PhysOrg, Science Daily, and many other online news sites.
       - Interviews on: The National Public Radio show “All Things Considered” (broadcast on 560 stations to ~12 million listners), CBS Radio Los Angeles,
   CBS Radio Washington DC, Canadian Broadcasting Centre, and KPCC Southern California Public Radio.

29. Ionic effects on viral DNA packaging and portal motor function in bacteriophage phi29
      D. N. Fuller, J. P. Rickgauer, P. J. Jardine, S. Grimes, D. L. Anderson, D. E. Smith,
      Proceedings of the National Academy of Sciences USA 104, 11245 (2007) (PDF file)
      - Highlighted in a commentary by M. Williams in PNAS (commentary). Highlighted by the editor in a summary in the front pages of the Journal (Highlight)
    - News articles: PhysOrg, Biology News Net, Medical News Today, Science Daily, Bio-medicine, UCSD

28. Self-diffusion of entangled linear and circular DNA molecules: Dependence on length and concentration
      R. M. Robertson and D. E. Smith
      Macromolecules 40, 3373 (2007) (PDF file)

27. A simple system for staining protein and nucleic acid electrophoresis gels
      D. M. Raymer, D. E. Smith,
      Electrophoresis 28, 746 (2007) (PDF file)

26. Strong effects of molecular topology on diffusion of entangled DNA molecules
      R. M. Robertson and D. E. Smith,
      Proceedings of the National Academy of Sciences USA 104, 4824 (2007)   (PDF file)

25. DNA as a metrology standard for length and force measurements with optical tweezers
      J. P. Rickgauer, D. N. Fuller, D. E. Smith,
      Biophysical Journal 91, 4253 (2006) (PDF file)

24. Dynamics of single DNA looping and cleavage by Sau3AI and effect of tension applied to the DNA
      G. J. Gemmen, R. Millin, D. E. Smith,
      Biophysical Journal 91, 4154 (2006) (PDF file)
- News articles: PhysOrg, Chemlin, Medical News Today, Science Daily, UCSD,

23. Single-Molecule Studies of DNA: Visualization and Manipulation of Individual DNA Molecules with Fluorescence Microscopy and Optical Tweezers
      J. P. Rickgauer and D. E. Smith,
      Book Chapter in "Soft Matter: Scattering, Imaging and Manipulation, Vol. 4, Edited by R. Borsali and R. Pecora, Springer (2007) (PDF file)

22. Tension-dependent DNA cleavage by restriction endonucleases: two-site enzymes are "switched off" at low force
      G.J. Gemmen, R. Millin, D. E. Smith,
      Proceedings of the National Academy of Sciences USA 103, 11555 (2006) (PDF file)

21. DNA looping by two-site restriction endonucleases: heterogeneous probability distributions for loop size and unbinding force
      G. J. Gemmen, R. Millin, D. E. Smith,
      Nucleic Acids Research 34, 2864 (2006) (PDF file) (supplemental data)

20. Preparation and Characterization of a Set of Linear DNA Molecules for Polymer Physics and Rheology Studies
      S. Laib, R. M. Robertson, and D. E. Smith,
      Macromolecules, 39, 4115 (2006) (PDF file)

19. Diffusion of isolated DNA molecules: Dependence on length and topology
      R.M. Robertson, S. Laib, D. E. Smith,
      Proceedings of the National Academy of Sciences USA, 103, 7310 (2006) (PDF file)

18. A general method for manipulating DNA sequences from any organism with optical tweezers
      D.N. Fuller, G.J. Gemmen, J.P. Rickgauer, A. Dupont, R. Millin, P. Recouvreux, D. E. Smith,
      Nucleic Acids Research 34, e15 (2006) (PDF file)

17. Forced Unraveling of Nucleosomes Assembled on Heterogeneous DNA Using Core Histones, NAP-1, and ACF
      G. J. Gemmen, R. Sim, K. A. Haushalter, P.C. Ke, J. T. Kadonaga, D. E. Smith,
      Journal of Molecular Biology 351, 89 (2005) (PDF file)

16. The Bacteriophage phi29 Portal Motor can Package DNA Against a Large Internal Force
      D. E. Smith, S. J. Tans, S. B. Smith, S. Grimes, D. L. Anderson, C. Bustamante,
      Nature 413, 748 (2001) (PDF file)
- Featured as the cover story (Cover image)

15. Dynamics of Dilute and Semidilute DNA solutions in the Start-up of Shear flow
      J. Hur, E. Shaqfeh, H. Babcock, D. E. Smith, S. Chu,
      Journal of Rheology 45, 421 (2001) (PDF file)

14. Single-Molecule Studies of DNA Mechanics
      C. Bustamante, S. B. Smith, J. T. Liphardt, D. E. Smith,
      Current Opinion in Structural Biology 10, 279 (2000) (PDF file)

13. Relating the Microscopic and Macroscopic Response of a Polymeric Fluid in a Shearing Flow
      H. P. Babcock, D. E. Smith, J. Hur, E. Shaqfeh, S. Chu,
      Physical Review Letters 85, 2018 (2000) (PDF file)

12. Single Polymer Dynamics in Steady Shear Flow
      D. E. Smith, H. P. Babcock, S. Chu,
      Science 283, 1724 (1999) (PDF file)

11. Brownian Dynamics Simulations of a DNA Molecule in an Elongational Flow Field
      R. G. Larson, H. Hu, D. E. Smith, S. Chu
      Journal of Rheology 43(2), 267 (1999) (PDF file)

10. Response of Flexible Polymers to a Sudden Elongational Flow
      D. E. Smith, S. Chu,
      Science 281, 1335 (1998) (PDF file)

9. Single Polymer Dynamics in an Elongational Flow
    T. T. Perkins, D. E. Smith, S. Chu,
     Science 276, 2016 (1997)   (PDF file)
     - Highlighted in a perspective by P.G. de Gennes in Science (Link)

8. Hydrodynamics of a DNA Molecule in a Flow Field
    R. G. Larson, T. T. Perkins, D. E. Smith, S. Chu,
    Physical Review E 55, 1794 (1997) (PDF file)

7. Dynamical Scaling of DNA Diffusion Coefficients
    D. E. Smith, T. T. Perkins, S. Chu,
    Macromolecules 29, 1372 (1996) (PDF file)

6. Self-Diffusion of an Entangled DNA Molecule by Reptation
    D. E. Smith, T. T. Perkins, S. Chu,
    Physical Review Letters 75, 4146 (1995) (PDF file)

5. Stretching of a Single Tethered Polymer in a Uniform Flow
    T. T. Perkins, D. E. Smith, R. G. Larson, S. Chu,
    Science 268, 83 (1995) (PDF file)

4. Direct Observation of Tube-like Motion of a Single Polymer Chain
    T. T. Perkins, D. E. Smith, S. Chu
    Science 264, 819, (1994) (PDF file)
- Featured as the cover story (Cover Image)
- News articles in the San Jose Mercury News, APS Physics News

3. Relaxation of a Single DNA Molecule Observed by Optical Microscopy
    T. T. Perkins, S. R. Quake, D. E. Smith, S. Chu,
    Science 264, 822 (1994) (PDF file)

2. Viscous Finger Narrowing at the Coil Stretch Transition in a Dilute Polymer Solution
    D. E. Smith, X. Z. Wu, A. Libchaber, E. Moses, T. Witten
    Physical Review A 45, 2165 (1992) (PDF file)

1. How to Generate Chaos at Home
    D. E. Smith,
    Scientific American (January 1992, p. 144) (PDF file)