User profiles for "author:Dudko O"

Olga Dudko

Professor of Physics, University of California San Diego
Verified email at physics.ucsd.edu
Cited by 4294

Intrinsic rates and activation free energies from single-molecule pulling experiments

OK Dudko, G Hummer, A Szabo�- Physical review letters, 2006 - APS
We present a unified framework for extracting kinetic information from single-molecule
pulling experiments at constant force or constant pulling speed. Our procedure provides�…

Theory, analysis, and interpretation of single-molecule force spectroscopy experiments

OK Dudko, G Hummer, A Szabo�- Proceedings of the�…, 2008 - National Acad Sciences
Dynamic force spectroscopy probes the kinetic and thermodynamic properties of single
molecules and molecular assemblies. Here, we propose a simple procedure to extract�…

Beyond the conventional description of dynamic force spectroscopy of adhesion bonds

OK Dudko, AE Filippov, J Klafter…�- Proceedings of the�…, 2003 - National Acad Sciences
Dynamic force spectroscopy of single molecules is described by a model that predicts a
distribution of rupture forces, the corresponding mean rupture force, and variance, which are�…

First-passage processes in the genome

Y Zhang, OK Dudko�- Annual review of biophysics, 2016 - annualreviews.org
Many essential processes in biology share a common fundamental step—establishing
physical contact between distant segments of DNA. How fast this step is accomplished sets�…

[HTML][HTML] Extracting kinetics from single-molecule force spectroscopy: nanopore unzipping of DNA hairpins

OK Dudko, J Math�, A Szabo, A Meller, G Hummer�- Biophysical journal, 2007 - cell.com
Single-molecule force experiments provide powerful new tools to explore biomolecular
interactions. Here, we describe a systematic procedure for extracting kinetic information from�…

[HTML][HTML] Global analysis of X-chromosome dosage compensation

V Gupta, M Parisi, D Sturgill, R Nuttall, M Doctolero…�- Journal of biology, 2006 - Springer
Background Drosophila melanogaster females have two X chromosomes and two autosome
sets (XX; AA), while males have a single X chromosome and two autosome sets (X; AA)�…

[HTML][HTML] 3D trajectories adopted by coding and regulatory DNA elements: first-passage times for genomic interactions

JS Lucas, Y Zhang, OK Dudko, C Murre�- Cell, 2014 - cell.com
During B lymphocyte development, immunoglobulin heavy-chain variable (VH), diversity
(DH), and joining (JH) segments assemble to generate a diverse antigen receptor repertoire�…

Pulling direction as a reaction coordinate for the mechanical unfolding of single molecules

RB Best, E Paci, G Hummer…�- The Journal of Physical�…, 2008 - ACS Publications
The folding and unfolding kinetics of single molecules, such as proteins or nucleic acids, can
be explored by mechanical pulling experiments. Determining intrinsic kinetic information, at�…

Decoding the mechanical fingerprints of biomolecules

OK Dudko�- Quarterly reviews of biophysics, 2016 - cambridge.org
The capacity of biological macromolecules to act as exceedingly sophisticated and highly
efficient cellular machines–switches, assembly factors, pumps, or motors–is realized through�…

Locating the barrier for folding of single molecules under an external force

OK Dudko, TGW Graham, RB Best�- Physical review letters, 2011 - APS
Single-molecule pulling experiments on the folding of biomolecules are usually interpreted
with one-dimensional models in which the dynamics occurs on the “pulling coordinate.”�…