Faculty Description

• ASSOCIATE PROFESSOR
• Ph. D., Stanford University, 1999
• Lab Phone:  822-1379 or 822-4836
• http://physics.ucsd.edu/~des
• RESEARCH: Biophysics

• Office Location:  NSB 2115
• Office Phone:  858-534-5241
• Email:  des0free(AT)gmail(DOT)com
• Administrative Contact:  Nancy Steinmetz

• - Mechanical manipulation and imaging of single DNA molecules
  - Viral DNA packaging in bacteriophages phi29, lambda, and T4
  - Function of ATP-dependent molecular motors
  - Single polymer dynamics (polymer physics, DNA properties, rheology)
  - Chromatin assembly and structure
  - Enzyme mediated DNA looping
  - Restriction endonuclease function
  - Physics of knot formation

• Honors and Awards
• - Sloan Foundation Fellow, 2003
  - Beckman Young Investigator Award, 2003
  - Searle Scholars Award, 2002
  - Burroughs Wellcome Fund Career Award in Biomedical Science, 2001
  - Research Corporation Research Innovation Award, 2001
  - Graduate Fellowship, NSF Program in Mathematics and Molecular Biology, 1996
  - Sigma Xi Science Prize, 1993
  - Elected to Phi Beta Kappa, 1993

• - A DNA Translocation Velocity Controller in a Viral Packaging Motor J. M. Tsay, J. Sippy, D. del Toro, B. T. Andrews, B. Draper, V. Rao, C. Catalano, M. Feiss, D. E. Smith, submitted (PDF file)


• - Biophysics of Knotting, D. Meluzzi, D. E. Smith, G. Arya, Annual Reviews of Biophysics, in press (PDF file)


• - 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)


• - 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)


• - 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)


• - 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)


• - 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)


• - 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)


• - 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)


• - 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)