Department of Physics

Faculty Description


  • ASSOCIATE PROFESSOR
  • Ph. D., Institute for Low Temperature Physics and Engineering, Kharkov, Ukraine, 2001
  • http://dudko.ucsd.edu/
  • RESEARCH: Biophysics
Contact
Research Statement
  • Motivated to discover physical rules that govern biological processes, we develop and apply methods of statistical physics to study living systems, arguably the most complex ones around. Currently, we are interested in the single-molecule approach which captures the dynamics of life at the scale of biological macromolecules, elucidating details that are typically lost when studied with traditional ('bulk') approaches. Our methods are analytical and numerical.
Awards & News
  • Professor Olga Dudko receives an NSF CAREER Award
  • UCSD physics Professor Olga Dudko has received an NSF Faculty Early Career Development Program (CAREER) Grant. The CAREER Program offers the National Science Foundation's most prestigious awards in support of junior faculty who exemplify the role of teacher-scholars through outstanding research, excellent education and the integration of education and research within the context of the mission of their organizations. Prof. Dudko received the award for her proposal to develop new theoretical approaches that will advance our understanding of fundamental physical principles that govern the structure formation and functioning of biological macromolecules at the single-molecule level. The proposed strategy is to use the great explanatory power of non-equilibrium physics to target for rapid advances the emerging field of single-molecule biophysics, and at the same time to motivate new physical concepts through the exploration of biological processes at the level of individual biomolecules. Prof. .Dudko's group uses theoretical and computational methods with the focus on quantitative, analytically tractable descriptions. More information on Prof. Dudko's research is available at http://dudko.ucsd.edu
  • CAREER Award, National Science Foundation 2009
  • CAREER Award, National Science Foundation 2009
  • Hellman Faculty Fellow 2009
  • Hellman Faculty Fellow 2009
  • NIH postdoctoral fellowship, National Institutes of Health 2003
  • NIH postdoctoral fellowship, National Institutes of Health 2003

  • Professor Dudko's PRL publication receives "Editor's suggestion" and is highlighted with a Synopsis on the American Physical Society website
  • UC San Diego physicist Olga Dudko and her colleagues at the University of Cambridge resolve a central discrepancy between theory and experiment regarding how molecules fold in response to applied forces.

    Single-molecule force spectroscopy, which measures how a molecule responds to mechanical forces pulling it apart, is an important tool in the study of biomolecules and other polymers. Experiments have shown that for weak forces molecules end up in two or more states, depending on the amount of stretching, which researchers attribute to how molecules fold and unfold. However, they have found it difficult to close in on a theoretical explanation. One recent study maintains that these experiments monitor a barrierless process, rather than one where the barrier is known to exist. It concluded that what the experiments are actually observing is merely the collapse of the molecules, and not folding per se.

    In their paper in Physical Review Letters, Olga Dudko at the University of California, San Diego, and co-workers appear to resolve this gap in our understanding of this fundamental mechanism in biomolecular interactions. From molecular simulation studies of molecular energy surfaces ("energy landscapes"), they find that there is indeed a barrier to folding, and it is this barrier that is probed by the experiments. It is just that the barrier appeared to be absent-hidden, as it were-in the earlier theoretical work, partly because of the method chosen to project a complicated, multidimensional folding scenario onto a single dimension (the "reaction coordinate"). A more robust choice of a folding coordinate ends up revealing the barrier.

    This resolution of a central discrepancy between theory and observations in the important field of molecular-particularly protein-folding should bring about a collective sigh of relief among many biological physicists and physical chemists. - Sami Mitra, Physical Review Letters, American Physical Society

    Link to the online publication: http://prl.aps.org/abstract/PRL/v107/i20/e208301

Selected Publications
  • - Dudko O.K., Mathe J., and Meller A. Nanopore Force Spectroscopy tools for analyzing single biomolecular complexes Methods in Enzymology (2010) in press.

  • - Suzuki Y. and Dudko O.K. Single-molecule rupture dynamics on multidimensional landscapes Physical Review Letters 104: 048101 (2010)

  • - Dudko O.K. Single-molecule mechanics: New insights from the escape-over-a-barrier problem Proc. Natl. Acad. Sci. USA 106: 8795-8796 (2009)

  • - Dudko O.K. and Meller A. Probing biomolecular interactions using nanopore force spectroscopy Encyclopedia of Analytical Chemistry, Ed. R. Meyers. John Wiley & Sons, Ltd. (2009)

  • - Dudko O.K., Hummer G., and Szabo A. Theory, analysis, and interpretation of single-molecule force spectroscopy experiments Proc. Natl. Acad. Sci. USA 105: 15755-15760 (2008)

  • - Best R.B., Paci E., Hummer G., and Dudko O.K. Pulling direction as a reaction coordinate for the mechanical unfolding of single molecules J.Phys.Chem. B 112: 5968-5976 (2008)

  • - Dudko O.K., Mathe J., Szabo A., Meller A., and Hummer G. Extracting kinetics from single-molecule force spectroscopy: Nanopore unzipping of DNA hairpins Biophys. J. 92: 4188-4195 (2007)

  • - Dudko O.K. Statistical Mechanics: Entropy, Order Parameters, and Complexity Journal of Statistical Physics 126 (book review) (2007)

  • - Dudko O.K., Hummer G., and Szabo A. Intrinsic Rates and Activation Free Energies from Single-Molecule Pulling Experiments Physical Review Letters 96: 108101 (2006)

  • - Gupta V., Parisi M., Sturgill D., Nuttall R., Doctolero M., Dudko O.K., Malley J.D., Eastman P.S., and Oliver B. Global analysis of X-chromosome dosage compensation Journal of Biology 5:3 (2006)