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Pierse C.A. and Dudko O.K.
Distinguishing signatures of multipathway conformational transitions
Physical Review Letters 118: 088101 (2017)

Zhang Y. and Dudko O.K.
First-passage processes in the genome
Annual Reviews of Biophysics 45:117-34 (2016)

Benichou I., Zhang Y., Dudko O.K., and Givli S.
The rate dependent response of a bistable chain at finite temperature
Journal of the Mechanics and Physics of Solids 95, 44-63 (2016)

Dudko O.K.
Decoding the mechanical fingerprints of biomolecules
Quarterly Reviews of Biophysics 49, e3, 1-14 (2015)

Zhang Y. and Dudko O.K.
Statistical mechanics of viral entry
Physical Review Letters 114: 018104 (2015)

Lucas J., Zhang Y., Dudko O.K. and Murre C.
3D Trajectories Adopted by Coding and Regulatory DNA Elements: First-Passage Times for Genomic Interactions
Cell 158, 339-352 (2014)

Garai A.*, Zhang Y.* and Dudko O.K.
Conformational dynamics through an intermediate [*equal contributions]
J. Chem. Phys. 140, 135101 (2014)

Pierse C.A. and Dudko O.K.
Kinetics and energetics of biomolecular folding and binding
Biophysical Journal -- Letter 105 (9): L19-L22 (2013)
... Highlighted by the Editor as New & Notable
... Selected for the "Best of 2013" reprint collection of the Biophysical Journal

Zhang Y. and Dudko O.K.
A transformation for the mechanical fingerprints of complex biomolecular interactions
Proc. Natl. Acad. Sci. USA 110 (41): 16432-16437 (2013)

Suzuki Y. and Dudko O.K.
Single molecules in an extension clamp: Extracting rates and activation barriers
Physical Review Letters 110: 158105 (2013)

Dudko O.K., Graham T.G.W., and Best R.B.
Locating the barrier for folding of single molecules under an external force
Physical Review Letters 107, 208301 (2011)
... Marked as an Editors' Suggestion
... Highlighted with a Synopsis in the online APS publication "Physics"

Suzuki Y. and Dudko O.K.
Biomolecules under mechanical stress: A simple mechanism of complex behavior
J. Chem. Phys. 134, 065102 (2011)

Dudko O.K., Mathe J., and Meller A.
Nanopore force spectroscopy tools for analyzing single biomolecular complexesi
Methods in Enzymology 475: 565-589 (2010)

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)
... Highlighted by the Editor as New and Notable

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)

Dudko O.K., Weiss G.H. and Chernomordik V.
Mean time-of-flight of photons in transillumination measurements of optically anisotropic tissue with an inclusion
Phys. Med. Biol. 51: 4719-4733 (2006)

Dudko O.K., Popov V.L., Putzar G.
Tribospectroscopy of randomly rough surfaces
Tribol. Int. 39: 456 (2006)

Dudko O.K., Szabo A., Ketter J., and Wightman M.
Analytic Theory of the Current at Inlaid Planar Ultramicroelectrodes: Comparison with Experiments on Elliptic Disks
J. Electroanalyt. Chem. 586: 18-22 (2006)

Dudko O.K., Berezhkovskii A.M., Weiss G.H.
Time-Dependent Diffusion Coefficients in Periodic Porous Materials
J. Phys. Chem. B 109: 21296-21299 (2005)

Dudko O.K. and Weiss G.H.
Photon diffusion in biological tissues
Diffusion Fundamentals 2: 114, Leipziger Universitätsverlag 2005)

Dudko O.K. and Weiss G.H.
Estimation of anisotropic optical parameters of tissue in a slab geometry
Biophys. J. 88: 3205-3211 (2005)

Dudko O.K. and Szabo A.
Time-dependent Rate Coefficients for Diffusion-Influenced Reactions with Centrosymmetric Potentials
J. Phys. Chem.B 109: 5891-5894 (2005)

Dudko O.K., Filippov A.E., Klafter J., and Urbakh M.
Following single molecules by force spectroscopy
Israel J. Chem. 44 (4): 363-372 (2004)

Dudko O.K., Berezhkovskii A.M., Weiss G.H.
Diffusion in the presence of periodically spaced permeable membranes
J. Chem. Phys. 121 (22): 11283-11288 (2004)

Dudko O.K., Weiss G.H., Chernomordik V., and Gandjbakhche A.H.
Photon migration in turbid media with anisotropic optical properties
Phys. Med. Biol. 49 (17): 3979-3989 (2004)

Dudko O.K., Berezhkovskii A.M., Weiss G.H.
Rate constant for diffusion-influenced ligand binding to receptors of arbitrary shape on a cell surface
J. Chem. Phys. 121 (3): 1562-1565 (2004)

Popov V.L., Dudko O.K.
Tribospectroscopy of surfaces with statistically random roughness
Tech. Phys. Lett. 30 (2): 148-150 (2004)

Dudko O.K., Filippov A.E., Klafter J., and Urbakh M.
Beyond the conventional description of dynamic force spectroscopy of adhesion bonds
Proc. Natl. Acad. Sci. USA 100 (20): 11378-11381 (2003)

Dudko O.K., Filippov A.E., Klafter J., and Urbakh M.
Manipulations of individual molecules by scanning probes
Nano Letters 3 (6): 795-798 (2003)

Dudko O.K., Filippov A.E., Klafter J., and Urbakh M.
Control of friction by shear induced phase transitions
Phys. Rev. B 66, 094114 (2002)

Dudko O.K., Filippov A.E., Klafter J., and Urbakh M.
Chemical control of friction: mixed lubricant monolayers
Trib. Lett. 12 (4), 217-227 (2002)

Dudko O.K. and Kovalev A.S.
Effect of roughness on the magnetic structure of ferro/antiferromagnetic inteface
J. Magn. Magn. Mater. 240, 321-324 (2002)

Dudko O.K., Filippov A.E., Klafter J., and Urbakh M.
Dynamic force spectroscopy: a Fokker-Planck approach
Chem. Phys. Lett. 352 (5-6), 499-504 (2002)

Dudko O.K. and Kovalev A.S.
Magnetostructural topological solitons in 2D antiferromagnet with a dislocation
Mater. Sci. Forum 373-3, 811-814 (2001)

Dudko O.K. and Kovalev A.S.
Influence of dislocations on the magnetic structure of two-dimensional anisotropic antiferromagnets
Low Temp. Phys. 26 (8), 603-608 (2000)

Dudko O.K. and Kovalev A.S.
The distribution of magnetization for a stepped ferro-antiferromagnet interface
Acta Phys. Pol. A 97 (3), 479-482 (2000)

Dudko O.K. and Kovalev A.S.
Magnetic ordering at the stepped ferro/antiferromagnetic interface
Low Temp. Phys. 25 (1), 18-23 (1999)

Dudko O.K. and Kovalev A.S.
Magnetostructural topological defects in two-dimensional antiferromagnets
Low Temp. Phys. 24 (6), 422-431 (1998)