Index: /qipapers.bib
===================================================================
--- /qipapers.bib	(revision 788)
+++ /qipapers.bib	(revision 789)
@@ -15714,3 +15714,7192 @@
   pages = {{131-135}},
   journal = {{Biomedical Papers}},
-  volume = {{147}
+  volume = {{147}},
+  author = {Dvor\\\'ak, Zdenek and Pascussi, Jean-Marc and Modriansk\\\'y, Martin}
+}
+@article{Medalion2010,
+  number = {{4}},
+  year = {2010},
+  title = {{Coupling of twist and writhe in short DNA loops
+ }},
+  pages = {{045101}},
+  journal = {{The Journal of Chemical Physics}},
+  volume = {{132}},
+  author = {Medalion, Shlomi and Rappaport, Shay M. and Rabin, Yitzhak}
+}
+@article{Cherif2006,
+  number = {{2}},
+  year = {2006},
+  title = {{Clinically Related Protein-Peptide Interactions Monitored in Real Time on Novel Peptide Chips by Surface Plasmon Resonance Imaging}},
+  pages = {{255-262}},
+  journal = {{Clinical Chemistry}},
+  volume = {{52}},
+  author = {Cherif, Boutheina and Roget, Andr\\\'e and Villiers, Christian L. and Calemczuk, Roberto and Leroy, Vincent and Marche, Patrice N. and Livache, Thierry and Villiers, Marie-Bernadette}
+}
+@article{Gibson1991,
+  number = {{10}},
+  year = {1991},
+  title = {{Experimental test of an analytical model of aberration in an oil-immersion objective lens used in three-dimensional light microscopy}},
+  pages = {{1601-1613}},
+  journal = {{Journal of the Optical Society of America A}},
+  volume = {{8}},
+  author = {Gibson, Sarah Frisken and Lanni, Frederick}
+}
+@misc{Bouchiat2007,
+  year = {2007},
+  title = {{Spatial Constraint Corrections to the Elasticity of dsDNA Measured with Magnetic Tweezers}},
+  author = {Bouchiat, C.}
+}
+@article{Bouchiat2006,
+  number = {{03}},
+  year = {2006},
+  title = {{Entropic elasticity of double-strand DNA subject to simple spatial constraints}},
+  pages = {{P03019}},
+  journal = {{Journal of Statistical Mechanics: Theory and Experiment}},
+  author = {Bouchiat, C.}
+}
+@article{Yoshinaga2002,
+  number = {{22}},
+  year = {2002},
+  title = {{Multiscaling in a long semiflexible polymer chain in two dimensions}},
+  journal = {{Journal of Chemical Physics}},
+  volume = {{116}},
+  author = {Yoshinaga, Natsuhiko and Yoshikawa, Kenichi and Kidoaki, Satoru}
+}
+@article{Sottas1999,
+  year = {1999},
+  title = {{Brownian Dynamics Simulation of DNA Condensation}},
+  pages = {{1858-1870}},
+  journal = {{Biophysical Journal}},
+  volume = {{77}},
+  author = {Sottas, Pierre-Edouard and Larquet, Eric and Stasiak, Andrzej and Dubochet, Jacques}
+}
+@article{Yamakawa1976a,
+  number = {{12}},
+  year = {1976},
+  title = {{Statistical mechanics of helical wormlike chains. I. Differential equations and moments}},
+  pages = {{5222-5228}},
+  journal = {{The Journal of Chemical Physics}},
+  volume = {{64}},
+  author = {Yamakawa, Hiromi and Fujii, Motoharu}
+}
+@article{Odijk1979,
+  year = {1979},
+  title = {{On the Ionic-Strength Dependence of the Intrinsic Viscosity of DNA}},
+  pages = {{3111-3113}},
+  journal = {{Biopolymers}},
+  volume = {{18}},
+  author = {Odijk, Theo}
+}
+@article{Sheppard1997,
+  number = {{3}},
+  year = {1997},
+  title = {{Effects of specimen refractive index on confocal imaging}},
+  pages = {{366-374}},
+  journal = {{Journal of Microscopy}},
+  volume = {{185}},
+  author = {Sheppard, C. J. R. and T\\\"or\\\"ok, P.}
+}
+@article{Vologodskii1994,
+  number = {{20}},
+  year = {1994},
+  title = {{DNA Extension under the Action of an External Force}},
+  pages = {{5623-5625}},
+  journal = {{Macromolecules}},
+  volume = {{27}},
+  author = {Vologodskii, Alexander}
+}
+@article{Rayleigh1919,
+  year = {1919},
+  title = {{On the problem of random vibrations, and of random flights in one, two, or three dimensions}},
+  pages = {{321-347}},
+  journal = {{Philosophical Magazine}},
+  volume = {{37}},
+  author = {Rayleigh, Lord}
+}
+@article{Lukic2007,
+  year = {2007},
+  title = {{Motion of a colloidal particle in an optical trap}},
+  pages = {{011112}},
+  journal = {{Physical Review E}},
+  volume = {{76}},
+  author = {{Luki\c{c}}, B. and Jeney, S. and Sviben, Z. and Kulik, A. and Florin, E.-L. and {Forr\'o}, L.}
+}
+@article{Storm2003a,
+  number = {{5}},
+  year = {2003},
+  title = {{The bend stiffness of S-DNA}},
+  pages = {{760-766}},
+  journal = {{Europhysics Letters (EPL)}},
+  volume = {{62}},
+  author = {Storm, C. and Nelson, P. C.}
+}
+@article{Odijk1977,
+  year = {1977},
+  title = {{Polyelectrolytes near the Rod Limit}},
+  pages = {{477-483}},
+  journal = {{Journal of Polymer Science: Polymer Physics Edition}},
+  volume = {{15}},
+  author = {Odijk, Theo}
+}
+@article{Beausang2007b,
+  year = {2007},
+  title = {{Diffusive hidden Markov model characterization of DNA looping dynamics in tethered particle experiments}},
+  journal = {{Physical Biology}},
+  author = {Beausang, John F. and Nelson, Philip C.}
+}
+@article{Fixman1973,
+  number = {{4}},
+  year = {1973},
+  title = {{Polymer conformational statistics. I. Probability distribution}},
+  pages = {{1553-1558}},
+  journal = {{The Journal of Chemical Physics}},
+  volume = {{58}},
+  author = {Fixman, Marshall and Alben, Richard}
+}
+@article{Gupta1993,
+  number = {{2}},
+  year = {1993},
+  title = {{Mean-field theory of phase transitions in liquid-crystalline polymers}},
+  pages = {{1588-1596}},
+  journal = {{Journal of Chemical Physics}},
+  volume = {{98}},
+  author = {Gupta, Anshu M. and Edwards, Sam F.}
+}
+@article{Butler2005,
+  year = {2005},
+  title = {{Brownian dynamics simulations of a flexible polymer chain which includes continuous resistance and multibody hydrodynamic interactions}},
+  journal = {{The Journal of Chemical Physics}},
+  volume = {{122}},
+  author = {Butler, Jason E. and Shaqfeh, Eric S.G.}
+}
+@article{Csiszar1991,
+  number = {{4}},
+  year = {1991},
+  title = {{Why Least Squares and Maximum Entropy? An Axiomatic Approach to Inference for Linear Inverse Problems}},
+  pages = {{2032-2066}},
+  journal = {{The Annals of Statistics}},
+  volume = {{19}},
+  author = {Csiszar, Imre}
+}
+@inproceedings{Dietrich2006,
+  year = {2006},
+  title = {{Advances in the Development of a Novel Method to be used in Proteomics using Gold Nanobeads}},
+  booktitle = {{Ultrasensitive and Single-Molecule Detection Technologies}},
+  editor = {Enderlein, J\\\"org and Gryczynski, Zygmunt K.},
+  volume = {{6092}},
+  publisher = {{Proceedings of SPIE}},
+  author = {Dietrich, Heidelinde R.C. and Young, Ian T. and Garini, Yuval}
+}
+@inproceedings{Dietrich2007,
+  year = {2007},
+  title = {A New Optical Method for Characterizing Single Molecule Interactions based on Dark Field Microscopy},
+  booktitle = {{Ultrasensitive and Single-Molecule Detection Technologies II}},
+  pages = {644403-1 - 64403-8},
+  editor = {Enderlein, J. and Gryczynski, Z.K.},
+  volume = {{6444}},
+  publisher = {{Proceedings of SPIE}},
+  author = {Dietrich, Heidelinde R.C. and Vermolen, Bart J. and Rieger, Bernd and Young, Ian T. and Garini, Yuval}
+}
+@article{Torok1996,
+  number = {{3}},
+  year = {1996},
+  title = {{Dark-field and differential phase contrast imaging modes in confocal microscopy using a half-aperture stop}},
+  pages = {{101-106}},
+  journal = {{Optik}},
+  volume = {{103}},
+  author = {T\\\"or\\\"ok, P. and Sheppard, C. J. R. and Laxzik, Z.}
+}
+@article{Dietrich2002,
+  number = {{1}},
+  year = {2002},
+  title = {{Relationship of Lipid Rafts to Transient Confinement Zones Detected by Single Particle Tracking}},
+  pages = {{274-284}},
+  journal = {{Biophysical Journal}},
+  volume = {{82}},
+  author = {Dietrich, Chrisian and Yang, Bing and Fujiwara, Takahiro and Kusumi, Akihiro and Jacobson, Ken}
+}
+@article{Schafer1991,
+  number = {{6334}},
+  year = {1991},
+  title = {{Transcription by single molecules of RNA polymerase observed by light microscopy}},
+  pages = {{444-448}},
+  journal = {{Nature}},
+  volume = {{352}},
+  author = {Schafer, Dorothy A. and Gelles, Jeff and Sheetz, Michael P. and Landick, Robert}
+}
+@book{Mazo2002,
+  series = {{International series of monographs on physics}},
+  year = {2002},
+  title = {{Brownian Motion: fluctuations, dynamics, and applications}},
+  address = {{Oxford}},
+  publisher = {{Clarendon Press}},
+  author = {Mazo, Robert M.}
+}
+@article{Deng2009,
+  number = {{10}},
+  year = {2009},
+  title = {{Effect of aberration on height calibration in three-dimensional localization-base microscoyp and particle tracking}},
+  pages = {{1886-1890}},
+  journal = {{Applied Optics}},
+  volume = {{48}},
+  author = {Deng, Yi. and Shaevitz, Joshua W.}
+}
+@article{Han2006,
+  year = {2006},
+  title = {{Brownian Motion of an Ellipsoid}},
+  journal = {{Science}},
+  volume = {{314}},
+  author = {Han, Y. and Alsayed, A.M. and Nobili, M. and Zhang, J. and Lubensky, T.C. and Yodh, A.G.}
+}
+@article{Dietrich2009,
+  year = {2009},
+  title = {Tethered Particle Motion Mediated by Scattering from Gold Nanoparticles and Darkfield Microscopy},
+  pages = {{031795}},
+  journal = {{Journal of Nanophotonics}},
+  volume = {{3}},
+  author = {Dietrich, Heidelinde R. C. and Rieger, Bernd and Wiertz, Frank G.M. and de Groote, Frederik H. and Heering, Hendrik A. and Young, Ian T. and Garini, Yuval}
+}
+@article{Shaevitz2007,
+  number = {{9}},
+  year = {2007},
+  title = {{Enhanced three-dimensional deconvolution microscopy using a measured depth-varying point-spread function}},
+  pages = {{2622-2627}},
+  journal = {{Journal of the Optical Society of America A}},
+  volume = {{24}},
+  author = {Shaevitz, Joshua W. and Fletcher, Daniel A.}
+}
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+  year = {1986},
+  title = {{The Theory of Polymer Dynamics}},
+  address = {{New York}},
+  publisher = {{Oxford University Press}},
+  author = {Doi, M. and Edwards, S.F. }
+}
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+  number = {{6}},
+  year = {2002},
+  title = {{Triple Minima in the Free Energy of Semiflexible Polymers}},
+  pages = {{065502}},
+  journal = {{Physical Review Letters}},
+  volume = {{89}},
+  author = {Dhar, Abhishek and Chaudhuri, Debasish}
+}
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+  number = {{6}},
+  year = {2004},
+  title = {{Information Bounsd and Optimal Analysis of Dynamic Single Molecule Measurements}},
+  pages = {{4015-4029}},
+  journal = {{Biophysical Journal}},
+  volume = {{86}},
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+}
+@article{Elburg2007,
+  number = {{1}},
+  year = {2007},
+  title = {{Improved correction of axial geometrical distortion in index-mismatched fluorescent confocal microscopic images using high-aperture objective lenses}},
+  pages = {{45-54}},
+  journal = {{Journal of Microscopy}},
+  volume = {{228}},
+  author = {Elburg, H.J. van and Kuypers, L.C. and Decraemer, W.F. and Dirckx, J.J.J.}
+}
+@phdthesis{Li2006,
+  year = {2006},
+  title = {{DNA entropic elasticity for short molecules attached to beads}},
+  author = {Li, Jinyu and Nelson, Philip C. and Betterton, M.D.}
+}
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+  series = {{Statistics: Textbooks and monographs}},
+  year = {1988},
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+  address = {{New York}},
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+}
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+  year = {2002},
+  title = {{Theoretical models for single-molecule DNA and RNA experiments: from elasticity to unzipping}},
+  pages = {{569-584}},
+  journal = {{Comptes rendus de l'Academie des Sciences Physique}},
+  volume = {{3}},
+  author = {Cocco, S. and Marko, J.F. and Monasson, R.}
+}
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+  year = {2003},
+  title = {{Force-extension behavior of folding polymers}},
+  pages = {{249-263}},
+  journal = {{The European Physical Journal E}},
+  volume = {{10}},
+  author = {Cocco, S. and Marko, J.F. and Monasson, R. and Sarkar, A. and Yan, J.}
+}
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+  year = {2001},
+  title = {{DNA microarrays for expression profiling}},
+  pages = {{21-25}},
+  journal = {{Current Opinion in Chemical Biology}},
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+  author = {Hughes, Timothy R. and Shoemaker, Daniel D.}
+}
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+  number = {{19}},
+  year = {1997},
+  title = {{Persistence Length of Single-Stranded DNA}},
+  pages = {{5763-5765}},
+  journal = {{Macromolecules}},
+  volume = {{30}},
+  author = {Tinland, Bernard and Pluen, Alain and Sturm, Jean and Weill, Gilbert}
+}
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+  year = {1951},
+  title = {{The Kolmogorov-Smirnov test for goodness of fit}},
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+  journal = {{Journal of the American Statistical Association}},
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+}
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+  year = {1993},
+  title = {{Semiflexible polymer in the half plane and statistics of the integral of a Brownian curve}},
+  pages = {{L1157-L1162}},
+  journal = {{Journal of Physics A: Mathematical and General}},
+  volume = {{26}},
+  author = {Burkhardt, Theodore W.}
+}
+@article{Stepanow2002,
+  number = {{4}},
+  year = {2002},
+  title = {{The distribution function of a semiflexible polymer and random walks with constraints}},
+  pages = {{546-551}},
+  journal = {{Europhysics Letters (EPL)}},
+  volume = {{60}},
+  author = {Stepanow, S. and Sch\\\"utz, G. M.}
+}
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+  number = {{5085}},
+  year = {1992},
+  title = {{Direct Mechanical Measurement of the Elasticity of Single DNA Molecules by Using Magnetic Beads}},
+  pages = {{1122-1126}},
+  journal = {{Science}},
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+}
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+  number = {{8}},
+  year = {2002},
+  title = {{High-Sensitivity Detection of DNA Hybridization on Microarrays Using Resonance Light Scattering}},
+  pages = {{1792-1979}},
+  journal = {{Analytical Chemistry}},
+  volume = {{74}},
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+}
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+  year = {1997},
+  title = {{Ionic effects on the elasticity of single DNA molecules}},
+  pages = {{6185-6190}},
+  journal = {{Proceedings of the National Academy of Sciences of the USA}},
+  volume = {{94}},
+  author = {Baumann, Christoph G. and Smith, Steven B. and Bloomfield, Victor A. and Bustamante, Carlos}
+}
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+  number = {{1}},
+  year = {1991},
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+  pages = {{103-118}},
+  journal = {{Journal of Colloid and Interface Science}},
+  volume = {{147}},
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+}
+@article{Blumberg2005,
+  year = {2005},
+  title = {{Three-Dimensional Characterization of Tethered Microspheres by Total Internal Reflection Fluorescence Microscopy}},
+  pages = {{1272-1281}},
+  journal = {{Biophysical Journal}},
+  volume = {{89}},
+  author = {Blumberg, Seth and Gajraj, Arivalagan and Pennington, Matthew W.}
+}
+@misc{Neumann2001,
+  month = {January 22, 2001},
+  year = {2001},
+  title = {{Entropic Elasticity of Weakly Perturbed Polymers}},
+  pages = {11},
+  publisher = {{The Energy Institute, The Pennsylvania State University}},
+  author = {Neumann, Richard M.}
+}
+@article{Ommering2010,
+  number = {{15}},
+  year = {2010},
+  title = {{Mobility and height detection of particle labels in an optical evanescent wave biosensor with single-label resolution}},
+  pages = {{155501}},
+  journal = {{Journal of Physics D: Applied Physics}},
+  volume = {{43}},
+  author = {van Ommering, Kim and Somers, Philip A. and Koets, Marjo and Schleipen, Jean J.H.B. and van Ijzendoorn, Leo J. and Prins, Menno W.J.}
+}
+@article{Heaton2001,
+  number = {{7}},
+  year = {2001},
+  title = {{Electrostatic surface plasmon resonance: Direct electric field-induced hybridization and denaturation in monolayer nucleic acid films and label-free discrimination of base mismatches}},
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+  journal = {{Proceedings of the National Academy of Sciences of the USA}},
+  volume = {{98}},
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+}
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+  number = {{7}},
+  year = {1972},
+  title = {{Statistical Mechanics of Wormlike Chains. I. Asymptotic Behavior}},
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+  journal = {{The Journal of Chemical Physics}},
+  volume = {{57}},
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+}
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+  number = {{4}},
+  year = {2001},
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+  pages = {{337-344}},
+  journal = {{The American Statistician}},
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+  author = {Henderson, Michael and Meyer, Mary C.}
+}
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+  number = {{9}},
+  year = {1994},
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+  journal = {{journal of Chemical Physics}},
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+}
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+  number = {{7}},
+  year = {1972},
+  title = {{Statistical Mechanics of Wormlike Chains. I. Asymptotic Behavior}},
+  pages = {{2839-2843}},
+  journal = {{The Journal of Chemical Physics}},
+  volume = {{57}},
+  author = {William, Gobush and Hiromi, Yamakawa and Stockmayer, W. H. and Magee, W. S.}
+}
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+  year = {1997},
+  title = {{Observation of Hybridization and Dehybridization of Thiol-Tethered DNA Using Two-Color Surface Plasmon Resonance Spectroscopy}},
+  pages = {{3401-3402}},
+  journal = {{Journal of the American Chemical Society}},
+  volume = {{119}},
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+}
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+  number = {{3}},
+  year = {2010},
+  title = {{A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality}},
+  pages = {{035105}},
+  journal = {{The Journal of Chemical Physics}},
+  volume = {{132}},
+  author = {Morriss-Andrews, Alex and Rottler, Joerg and Plotkin, Steven S.}
+}
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+  number = {{1}},
+  year = {1943},
+  title = {{Stochastic Problems in Physics and Astronomy}},
+  pages = {{2-87}},
+  journal = {{Revieuws of Modern Physics}},
+  volume = {{15}},
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+}
+@inproceedings{Ram2005,
+  series = {{Proceedings of SPIE}},
+  year = {2005},
+  title = {{How accurately can a single molecule be localized in three dimensions using a fluorescence microscope?}},
+  booktitle = {{Imaging, Manipulation and Analysis of Biomolecule and Cells: Fundamentals and Applications III}},
+  pages = {426-435},
+  volume = {{5699}},
+  author = {Ram, Sripad and Ward, E. Sally and Ober, Raimond J.}
+}
+@book{Papoulis1991,
+  series = {{McGraw-Hill series in electrical engineering, Communications and signal processing}},
+  edition = {{Third edition}},
+  year = {1991},
+  title = {{Probability, random variables, and stochastic processes}},
+  address = {{Singapore}},
+  publisher = {{McGraw-Hill}},
+  author = {Papoulis, Athanasios}
+}
+@inproceedings{Ram2007,
+  year = {2007},
+  title = {{A novel approach to determining the three-dimensional location of microscopic objects with applications to 3D particle tracking}},
+  booktitle = {{Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XIV}},
+  pages = {64430D},
+  editor = {Conchello, Jose-Angel and Cogswell, Carol J. and Wilson, Tony},
+  volume = {{6443}},
+  publisher = {{Proceedings of SPIE}},
+  author = {Ram, Sripad and Chao, Jerry and Prabhat, Prashant and Ward, E. Sally and Ober, Raimond J.}
+}
+@article{Wu2005,
+  year = {2005},
+  title = {{Three-dimensional fluorescent particle tracking at micron-scale using a single camera}},
+  pages = {{461-465}},
+  journal = {{Experiments in Fluids}},
+  volume = {{38}},
+  author = {Wu, Mingming and Roberts, John W. and Buckley, Mark}
+}
+@article{Maier2000,
+  number = {{22}},
+  year = {2000},
+  title = {{Replication by a single DNA polymerase of a stretched single-stranded DNA}},
+  pages = {{12002-12007}},
+  journal = {{Proceedings of the National Academy of Sciences of the USA}},
+  volume = {{97}},
+  author = {Maier, Berenike and Bensimon, David and Croquette, Vincent}
+}
+@misc{Odijk2005,
+  month = {August 4, 2005},
+  year = {2005},
+  title = {{Note on DNA grafted to a surface (experiments Heidi Dietrich, TU Delft)}},
+  author = {Odijk, Theo}
+}
+@article{Zimm1956,
+  number = {{2}},
+  year = {1956},
+  title = {{Dynamics of Polymer Molecules in Dilute Solution: Viscoelasticity, Flow Birefringence and Dielectric Loss}},
+  pages = {{269-278}},
+  journal = {{The Journal of Chemical Physics}},
+  volume = {{24}},
+  author = {Zimm, Bruno H.}
+}
+@article{Sadr2007,
+  year = {2007},
+  title = {{Diffusion-induced bias in near-wall velocimetry}},
+  pages = {{443-456}},
+  journal = {{Journal of Fluid Mechanics}},
+  volume = {{577}},
+  author = {Sadr, Reza and Hohenegger, Christel and Li, Haifeng and Mucha, Peter J. and Yoda, Minami}
+}
+@article{Qian2000b,
+  number = {{1}},
+  year = {2000},
+  title = {{Single-Particle Tracking: Brownian Dynamics of Viscoelastic Materials}},
+  pages = {{137-143}},
+  journal = {{Biophysical Journal}},
+  volume = {{79}},
+  author = {Qian, Hong}
+}
+@article{Pirrung2002,
+  number = {{8}},
+  year = {2002},
+  title = {{How to Make a DNA Chip}},
+  pages = {{1276-1289}},
+  journal = {{Angewandte Chemie International Edition}},
+  volume = {{41}},
+  author = {Pirrung, Michael C.}
+}
+@article{Marko2003,
+  number = {{3}},
+  year = {2003},
+  title = {{The micromechanics of DNA}},
+  journal = {{Physics World}},
+  volume = {{16}},
+  author = {Marko, John F. and Cocco, Simona}
+}
+@article{Qian2000a,
+  number = {{4}},
+  year = {2000},
+  title = {{A mathematical analysis for the Brownian dynamics of a DNA tether}},
+  pages = {{331-340}},
+  journal = {{Journal of Mathematical Biology}},
+  volume = {{41}},
+  author = {Qian, Hong}
+}
+@misc{Marko2005,
+  month = {June 2, 2005},
+  year = {2005},
+  title = {{Introduction to Single-DNA Micromechanics}},
+  pages = {63},
+  publisher = {{Department of Physics, University of Illinois at Chicago}},
+  author = {Marko, J.F.}
+}
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