Changeset 108


Ignore:
Timestamp:
10/08/10 16:18:30 (15 years ago)
Author:
qipapers
Message:

commit via qipapers

File:
1 edited

Legend:

Unmodified
Added
Removed
  • qipapers.bib

    r107 r108  
    1245312453  year = {2010}
    1245412454}
    12455 @proceedings{Brinkers2010,
     12455@inproceedings{Brinkers2010,
     12456  author = {Brinkers, Sanneke and Dietrich, Heidelinde R. C. and Stallinga, Sjoerd and Mes, Jurriaan J. and Young, Ian T. and Rieger, Bernd},
    1245612457  title = {Single Molecule Detection Of Tuberculosis Nucleic Acid Using Dark Field Tethered Particle Motion},
    1245712458  year = {2010},
     12459  pages = {1269},
    1245812460  month = {April 14-17},
    1245912461  address = {Rotterdam, The Netherlands},
    12460   organization = {IEEE International Symposium on Biomedical Imaging}
     12462  booktitle = {IEEE International Symposium on Biomedical Imaging}
    1246112463}
    1246212464@article{Cordes2010,
     
    1546515467@article{Meyer2008,
    1546615468  author = {Meyer, J.C. and Girit, C.O. and Crommie, M.F. and Zettl, A.},
    15467   title = {Imaging a
     15469  title = {Imaging and dynamics of light atoms and molecules on graphene},
     15470  journal = {Nature},
     15471  year = {2008},
     15472  volume = {454},
     15473  pages = {319-323}
     15474}
     15475@article{Muller2006,
     15476  author = {Muller, D.A. and Kirkland, E.J. and Thomas, M.G. and Grazul, J.L. and Fitting, L. and Weyland, M.},
     15477  title = {Room design for high-performance electron microscopy},
     15478  journal = {Ultramicroscopy},
     15479  year = {2006},
     15480  volume = {106},
     15481  pages = {1033-1040}
     15482}
     15483@article{Xing2009,
     15484  author = {Xing, Q. and Lograsso, T.A.},
     15485  title = {A rapid method to correct objective lens astigmatism in a TEM},
     15486  journal = {Ultramicroscopy},
     15487  year = {2009},
     15488  volume = {109},
     15489  pages = {287-290}
     15490}
     15491@article{Nellist1998a,
     15492  author = {Nellist, P.D. and Pennycook, S.J.},
     15493  title = {Accurate structure determination from image reconstruction in {ADF} {STEM}},
     15494  journal = {Journal of Microscopy},
     15495  year = {1998},
     15496  volume = {1-2},
     15497  pages = {159-170}
     15498}
     15499@article{Schaffer2009,
     15500  author = {Schaffer, B. and Hohenester, U. and Truegler, A. and Hofer, F.},
     15501  title = {High-resolution surface plasmon imaging of gold nanoparticles by energy-filtered transmission electron microscopy},
     15502  journal = {Physical Review B},
     15503  year = {2009},
     15504  volume = {79},
     15505  pages = {041401}
     15506}
     15507@inproceedings{Rieger2008,
     15508  author = {Rieger, B. and Veen, G.N.A. van},
     15509  title = {Method to determine image sharpness and resolution
     15510in Scanning Electron Microscopy images},
     15511  year = {2008},
     15512  pages = {613-614},
     15513  month = {September 1-5},
     15514  editor = {Luysberg, M. and Tillmann, K. and Weirich, T.},
     15515  publisher = {Springer Verlag},
     15516  address = {Berline},
     15517  booktitle = {EMC 2008, Vol.1: Instrumentation and Methods}
     15518}
     15519@mastersthesis{Smith2009,
     15520  author = {Smith, S.C.},
     15521  title = {Improving single molecule
     15522fluorescence superresolution techniques},
     15523  year = {2009},
     15524  school = {Delft University of Technology}
     15525}
     15526@mastersthesis{Vroonland2010,
     15527  author = {Vroonland, S.},
     15528  title = {Superresolution Using Blinking Emitters},
     15529  year = {2010},
     15530  month = {June},
     15531  address = {Delft, The Netherlands},
     15532  school = {Delft University of Technology}
     15533}
     15534@article{Hell2009,
     15535  author = {Hell, S.W.},
     15536  title = {Microscopy and its focal switch},
     15537  journal = {Nature Methods},
     15538  year = {2009},
     15539  volume = {6},
     15540  pages = {24-32}
     15541}
     15542@article{Small2009,
     15543  author = {Small, A.R.},
     15544  title = {Theoretical Limits on Errors and Acquisition Rates in Localizing Switchable Fluorophores},
     15545  journal = {Biophysical Journal - Biophysical Letters},
     15546  year = {2009},
     15547  volume = {92},
     15548  number = {2},
     15549  pages = {L16-L18}
     15550}
     15551@article{Podczeck1997,
     15552  author = {Podczeck, F.},
     15553  title = {A shape factor to assess the shape of particles using image analysis},
     15554  journal = {Powder Technology},
     15555  year = {1997},
     15556  volume = {93},
     15557  pages = {47-53}
     15558}
     15559@article{Shaner2004,
     15560  author = {Shaner, N.C. and Campbell, R.E. and Steinbach, P.A. and Giepmans, B.N.G. and Palmer, A.E. and Tsien, R.Y.},
     15561  title = {Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein},
     15562  journal = {Nature Biotechnology},
     15563  year = {2004},
     15564  volume = {22},
     15565  number = {12},
     15566  pages = {1567-1672}
     15567}
     15568@article{Sader2010,
     15569  author = {Sader, K. and Brown, A. and Brydon, R. and Bleloch, A.},
     15570  title = {Quantitativ eanalysis of image contrast in phase contrast STEM for low dose imaging},
     15571  journal = {Ultramicroscopy},
     15572  year = {2010},
     15573  volume = {110},
     15574  pages = {1324-1331}
     15575}
     15576@article{Aert2010,
     15577  author = {Aert, s. van and Chen, J.H. and Dyck, D. van},
     15578  title = {Linear versus non-linear structural information limit in high-resolution transmission electron microscopy},
     15579  journal = {Ultramicroscopy},
     15580  year = {2010},
     15581  volume = {110},
     15582  pages = {1404-1410}
     15583}
     15584@article{Donzel2001,
     15585  author = {Donzel, Christian and Geissler, Matthias and Bernard, Andr\\\'e and Wolf, Heiko and Michel, Bruno and Hilborn, J\\\"ons and Delamarche, Emmanuel},
     15586  title = {{Hydrophilic Poly(dimethylsiloxane) Stamps for Microcontact Printing}},
     15587  journal = {{Advanced Materials}},
     15588  year = {2001},
     15589  volume = {{13}},
     15590  number = {{15}}
     15591}
     15592@article{Wang1997,
     15593  author = {Wang, Michelle D. and Yin, Hong and Landick, Robert and Gelles, Jeff and Block, Steven M.},
     15594  title = {{Stretching DNA with Optical Tweezers}},
     15595  journal = {{Biophysical Journal}},
     15596  year = {1997},
     15597  volume = {{72}},
     15598  number = {{3}},
     15599  pages = {{1335-1346}}
     15600}
     15601@article{Blanchard1999,
     15602  author = {Blanchard, Paul M.
     15603 Greenaway, Alan H.},
     15604  title = {{Simultaneous multiplane imaging with a distorted diffraction grating}},
     15605  journal = {{Applied Optics}},
     15606  year = {1999},
     15607  volume = {{38}},
     15608  number = {{32}},
     15609  pages = {{6692-6699}}
     15610}
     15611@article{Eversole2007,
     15612  author = {Eversole, D. and Luk'Yanchuk, B. and Ben-Yakar, A.},
     15613  title = {{Plasmonic laser nanoablation of silicon by the scattering of femtosecond pulses near gold nanospheres}},
     15614  journal = {{Applied Physics A}},
     15615  year = {2007},
     15616  volume = {{89}},
     15617  pages = {{283-291}}
     15618}
     15619@article{Dessinges2002,
     15620  author = {Dessinges, M. N. and Maier, B. and Zhang, Y. and Peliti, M. and Bensimon, D. and Croquette, V.},
     15621  title = {{Stretching Single Stranded DNA, a Model Polyelectrolyte}},
     15622  journal = {{Physical Review Letters}},
     15623  year = {2002},
     15624  volume = {{89}},
     15625  number = {{24}},
     15626  pages = {{248102-248106}}
     15627}
     15628@article{Taylor1990,
     15629  author = {Taylor, William H. and Hagerman, Paul J.},
     15630  title = {{Application of the Method of Phage T4 DNA Ligase-catalyzed Ring-closure to the Study of DNA Structure}},
     15631  journal = {{Journal of Molecular Biology}},
     15632  year = {1990},
     15633  volume = {{212}},
     15634  number = {{2}},
     15635  pages = {{363-376}}
     15636}
     15637@article{Uhlenbeck1930,
     15638  author = {Uhlenbeck, G.E. and Ornstein, L.S.},
     15639  title = {{On the Theory of the Brownian Motion}},
     15640  journal = {{Physical Review}},
     15641  year = {1930},
     15642  volume = {{36}}
     15643}
     15644@article{Yguerabide2001,
     15645  author = {Yguerabide, Juan and Yguerabide, Evangelina E.},
     15646  title = {{Resonance Light Scattering Particles as Ultrasensitive Labels for Detection of Analytes in a Wide Range of Applications}},
     15647  journal = {{Journal of Cellular Biochemistry Supplement}},
     15648  year = {2001},
     15649  volume = {{84}},
     15650  number = {{S37}},
     15651  pages = {{71-81}}
     15652}
     15653@article{Samuel2002,
     15654  author = {Samuel, Joseph and Sinha, Supurna},
     15655  title = {{Elasticity of semiflexible polymers}},
     15656  journal = {{Physical Review E}},
     15657  year = {2002},
     15658  volume = {{66}},
     15659  pages = {{050801}}
     15660}
     15661@article{Porschke1991,
     15662  author = {Porschke, Dietmar},
     15663  title = {{Persistence length and bending dynamics of DNA from electrooptical measurements at high salt concentrations}},
     15664  journal = {{Biophysical Chemistry}},
     15665  year = {1991},
     15666  volume = {{40}},
     15667  pages = {{169-179}}
     15668}
     15669@article{Schutz2000,
     15670  author = {Sch\\\"utz, Gerhard J. and Pastushenko, Vassili, Ph. and Gruber, Hermann J. and Knaus, Hans-G\\\"unter and Pragl, Bernt and Schindler, Hansgeorg},
     15671  title = {{3D Imaging of Individual Ion Channels in Live Cells at 40 nm Resolution}},
     15672  journal = {{Single Molecules}},
     15673  year = {2000},
     15674  volume = {{1}},
     15675  number = {{1}},
     15676  pages = {{25-31}}
     15677}
     15678@incollection{Vilfan2009,
     15679  author = {Vilfan, I.D. and Lipfert, J. and Koster, D.A. and Lemay, S.G. and Dekker, N.H.},
     15680  title = {{Magnetic Tweezers for Single-Molecule Experiments}},
     15681  year = {2009},
     15682  editor = {Hinterdorfer, P. and A., van Oijen},
     15683  publisher = {{Springer Science+Business Media}},
     15684  booktitle = {{Springer Handbook of Single-Molecule Biophysics}}
     15685}
     15686@article{Dvorak2003,
     15687  author = {Dvor\\\'ak, Zdenek and Pascussi, Jean-Marc and Modriansk\\\'y, Martin},
     15688  title = {{Approaches to Messenger RNA Detection - Comparison of Methods}},
     15689  journal = {{Biomedical Papers}},
     15690  year = {2003},
     15691  volume = {{147}},
     15692  number = {{2}},
     15693  pages = {{131-135}}
     15694}
     15695@article{Medalion2010,
     15696  author = {Medalion, Shlomi and Rappaport, Shay M. and Rabin, Yitzhak},
     15697  title = {{Coupling of twist and writhe in short DNA loops
     15698 }},
     15699  journal = {{The Journal of Chemical Physics}},
     15700  year = {2010},
     15701  volume = {{132}},
     15702  number = {{4}},
     15703  pages = {{045101}}
     15704}
     15705@article{Cherif2006,
     15706  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},
     15707  title = {{Clinically Related Protein-Peptide Interactions Monitored in Real Time on Novel Peptide Chips by Surface Plasmon Resonance Imaging}},
     15708  journal = {{Clinical Chemistry}},
     15709  year = {2006},
     15710  volume = {{52}},
     15711  number = {{2}},
     15712  pages = {{255-262}}
     15713}
     15714@article{Gibson1991,
     15715  author = {Gibson, Sarah Frisken and Lanni, Frederick},
     15716  title = {{Experimental test of an analytical model of aberration in an oil-immersion objective lens used in three-dimensional light microscopy}},
     15717  journal = {{Journal of the Optical Society of America A}},
     15718  year = {1991},
     15719  volume = {{8}},
     15720  number = {{10}},
     15721  pages = {{1601-1613}}
     15722}
     15723@misc{Bouchiat2007,
     15724  author = {Bouchiat, C.},
     15725  title = {{Spatial Constraint Corrections to the Elasticity of dsDNA Measured with Magnetic Tweezers}},
     15726  year = {2007}
     15727}
     15728@article{Bouchiat2006,
     15729  author = {Bouchiat, C.},
     15730  title = {{Entropic elasticity of double-strand DNA subject to simple spatial constraints}},
     15731  journal = {{Journal of Statistical Mechanics: Theory and Experiment}},
     15732  year = {2006},
     15733  number = {{03}},
     15734  pages = {{P03019}}
     15735}
     15736@article{Yoshinaga2002,
     15737  author = {Yoshinaga, Natsuhiko and Yoshikawa, Kenichi and Kidoaki, Satoru},
     15738  title = {{Multiscaling in a long semiflexible polymer chain in two dimensions}},
     15739  journal = {{Journal of Chemical Physics}},
     15740  year = {2002},
     15741  volume = {{116}},
     15742  number = {{22}}
     15743}
     15744@article{Sottas1999,
     15745  author = {Sottas, Pierre-Edouard and Larquet, Eric and Stasiak, Andrzej and Dubochet, Jacques},
     15746  title = {{Brownian Dynamics Simulation of DNA Condensation}},
     15747  journal = {{Biophysical Journal}},
     15748  year = {1999},
     15749  volume = {{77}},
     15750  pages = {{1858-1870}}
     15751}
     15752@article{Yamakawa1976a,
     15753  author = {Yamakawa, Hiromi and Fujii, Motoharu},
     15754  title = {{Statistical mechanics of helical wormlike chains. I. Differential equations and moments}},
     15755  journal = {{The Journal of Chemical Physics}},
     15756  year = {1976},
     15757  volume = {{64}},
     15758  number = {{12}},
     15759  pages = {{5222-5228}}
     15760}
     15761@article{Odijk1979,
     15762  author = {Odijk, Theo},
     15763  title = {{On the Ionic-Strength Dependence of the Intrinsic Viscosity of DNA}},
     15764  journal = {{Biopolymers}},
     15765  year = {1979},
     15766  volume = {{18}},
     15767  pages = {{3111-3113}}
     15768}
     15769@article{Sheppard1997,
     15770  author = {Sheppard, C. J. R. and T\\\"or\\\"ok, P.},
     15771  title = {{Effects of specimen refractive index on confocal imaging}},
     15772  journal = {{Journal of Microscopy}},
     15773  year = {1997},
     15774  volume = {{185}},
     15775  number = {{3}},
     15776  pages = {{366-374}}
     15777}
     15778@article{Vologodskii1994,
     15779  author = {Vologodskii, Alexander},
     15780  title = {{DNA Extension under the Action of an External Force}},
     15781  journal = {{Macromolecules}},
     15782  year = {1994},
     15783  volume = {{27}},
     15784  number = {{20}},
     15785  pages = {{5623-5625}}
     15786}
     15787@article{Rayleigh1919,
     15788  author = {Rayleigh, Lord},
     15789  title = {{On the problem of random vibrations, and of random flights in one, two, or three dimensions}},
     15790  journal = {{Philosophical Magazine}},
     15791  year = {1919},
     15792  volume = {{37}},
     15793  pages = {{321-347}}
     15794}
     15795@article{Lukic2007,
     15796  author = {Luki\\\c{c}, Branimir and Jeney, Sylvia and Sviben, Zeljko and Kulik, Andrzej and Florin, Ernst-Ludwig and Forr\\\'o, L\\\'aszl\\\'o},
     15797  title = {{Motion of a colloidal particle in an optical trap}},
     15798  journal = {{Physical Review E}},
     15799  year = {2007},
     15800  volume = {{76}},
     15801  pages = {{011112}}
     15802}
     15803@article{Storm2003a,
     15804  author = {Storm, C. and Nelson, P. C.},
     15805  title = {{The bend stiffness of S-DNA}},
     15806  journal = {{Europhysics Letters (EPL)}},
     15807  year = {2003},
     15808  volume = {{62}},
     15809  number = {{5}},
     15810  pages = {{760-766}}
     15811}
     15812@article{Odijk1977,
     15813  author = {Odijk, Theo},
     15814  title = {{Polyelectrolytes near the Rod Limit}},
     15815  journal = {{Journal of Polymer Science: Polymer Physics Edition}},
     15816  year = {1977},
     15817  volume = {{15}},
     15818  pages = {{477-483}}
     15819}
     15820@article{Beausang2007b,
     15821  author = {Beausang, John F. and Nelson, Philip C.},
     15822  title = {{Diffusive hidden Markov model characterization of DNA looping dynamics in tethered particle experiments}},
     15823  journal = {{Physical Biology}},
     15824  year = {2007}
     15825}
     15826@article{Fixman1973,
     15827  author = {Fixman, Marshall and Alben, Richard},
     15828  title = {{Polymer conformational statistics. I. Probability distribution}},
     15829  journal = {{The Journal of Chemical Physics}},
     15830  year = {1973},
     15831  volume = {{58}},
     15832  number = {{4}},
     15833  pages = {{1553-1558}}
     15834}
     15835@article{Gupta1993,
     15836  author = {Gupta, Anshu M. and Edwards, Sam F.},
     15837  title = {{Mean-field theory of phase transitions in liquid-crystalline polymers}},
     15838  journal = {{Journal of Chemical Physics}},
     15839  year = {1993},
     15840  volume = {{98}},
     15841  number = {{2}},
     15842  pages = {{1588-1596}}
     15843}
     15844@article{Butler2005,
     15845  author = {Butler, Jason E. and Shaqfeh, Eric S.G.},
     15846  title = {{Brownian dynamics simulations of a flexible polymer chain which includes continuous resistance and multibody hydrodynamic interactions}},
     15847  journal = {{The Journal of Chemical Physics}},
     15848  year = {2005},
     15849  volume = {{122}}
     15850}
     15851@article{Csiszar1991,
     15852  author = {Csiszar, Imre},
     15853  title = {{Why Least Squares and Maximum Entropy? An Axiomatic Approach to Inference for Linear Inverse Problems}},
     15854  journal = {{The Annals of Statistics}},
     15855  year = {1991},
     15856  volume = {{19}},
     15857  number = {{4}},
     15858  pages = {{2032-2066}}
     15859}
     15860@inproceedings{Dietrich2006,
     15861  author = {Dietrich, Heidelinde R.C. and Young, Ian T. and Garini, Yuval},
     15862  title = {{Advances in the Development of a Novel Method to be used in Proteomics using Gold Nanobeads}},
     15863  year = {2006},
     15864  volume = {{6092}},
     15865  editor = {Enderlein, J\\\"org and Gryczynski, Zygmunt K.},
     15866  publisher = {{Proceedings of SPIE}},
     15867  booktitle = {{Ultrasensitive and Single-Molecule Detection Technologies}}
     15868}
     15869@inproceedings{Dietrich2007,
     15870  author = {Dietrich, Heidelinde R.C. and Vermolen, Bart J. and Rieger, Bernd and Young, Ian T. and Garini, Yuval},
     15871  title = {{A New Optical Method for Characterizing Single Molecule Interactions based on Dark Field Microscopy}},
     15872  year = {2007},
     15873  volume = {{6444}},
     15874  pages = {644403-1 - 64403-8},
     15875  editor = {Enderlein, J\\\"org and Gryczynski, Zygmunt K.},
     15876  publisher = {{Proceedings of SPIE}},
     15877  booktitle = {{Ultrasensitive and Single-Molecule Detection Technologies II}}
     15878}
     15879@article{Torok1996,
     15880  author = {T\\\"or\\\"ok, P. and Sheppard, C. J. R. and Laxzik, Z.},
     15881  title = {{Dark-field and differential phase contrast imaging modes in confocal microscopy using a half-aperture stop}},
     15882  journal = {{Optik}},
     15883  year = {1996},
     15884  volume = {{103}},
     15885  number = {{3}},
     15886  pages = {{101-106}}
     15887}
     15888@article{Dietrich2002,
     15889  author = {Dietrich, Chrisian and Yang, Bing and Fujiwara, Takahiro and Kusumi, Akihiro and Jacobson, Ken},
     15890  title = {{Relationship of Lipid Rafts to Transient Confinement Zones Detected by Single Particle Tracking}},
     15891  journal = {{Biophysical Journal}},
     15892  year = {2002},
     15893  volume = {{82}},
     15894  number = {{1}},
     15895  pages = {{274-284}}
     15896}
     15897@article{Schafer1991,
     15898  author = {Schafer, Dorothy A. and Gelles, Jeff and Sheetz, Michael P. and Landick, Robert},
     15899  title = {{Transcription by single molecules of RNA polymerase observed by light microscopy}},
     15900  journal = {{Nature}},
     15901  year = {1991},
     15902  volume = {{352}},
     15903  number = {{6334}},
     15904  pages = {{444-448}}
     15905}
     15906@book{Mazo2002,
     15907  author = {Mazo, Robert M.},
     15908  title = {{Brownian Motion: fluctuations, dynamics, and applications}},
     15909  year = {2002},
     15910  publisher = {{Clarendon Press}},
     15911  series = {{International series of monographs on physics}},
     15912  address = {{Oxford}}
     15913}
     15914@article{Deng2009,
     15915  author = {Deng, Yi. and Shaevitz, Joshua W.},
     15916  title = {{Effect of aberration on height calibration in three-dimensional localization-base microscoyp and particle tracking}},
     15917  journal = {{Applied Optics}},
     15918  year = {2009},
     15919  volume = {{48}},
     15920  number = {{10}},
     15921  pages = {{1886-1890}}
     15922}
     15923@article{Han2006,
     15924  author = {Han, Y. and Alsayed, A.M. and Nobili, M. and Zhang, J. and Lubensky, T.C. and Yodh, A.G.},
     15925  title = {{Brownian Motion of an Ellipsoid}},
     15926  journal = {{Science}},
     15927  year = {2006},
     15928  volume = {{314}}
     15929}
     15930@article{Dietrich2009,
     15931  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},
     15932  title = {{Tethered Particle Motion Mediated by Scattering from Gold Nanoparticles and Darkfield Microscopy}},
     15933  journal = {{Journal of Nanophotonics}},
     15934  year = {2009},
     15935  volume = {{3}},
     15936  pages = {{031795}}
     15937}
     15938@article{Shaevitz2007,
     15939  author = {Shaevitz, Joshua W. and Fletcher, Daniel A.},
     15940  title = {{Enhanced three-dimensional deconvolution microscopy using a measured depth-varying point-spread function}},
     15941  journal = {{Journal of the Optical Society of America A}},
     15942  year = {2007},
     15943  volume = {{24}},
     15944  number = {{9}},
     15945  pages = {{2622-2627}}
     15946}
     15947@book{Doi1986,
     15948  author = {Doi, M. and Edwards, S.F. },
     15949  title = {{The Theory of Polymer Dynamics}},
     15950  year = {1986},
     15951  publisher = {{Oxford University Press}},
     15952  address = {{New York}}
     15953}
     15954@article{Dhar2002,
     15955  author = {Dhar, Abhishek and Chaudhuri, Debasish},
     15956  title = {{Triple Minima in the Free Energy of Semiflexible Polymers}},
     15957  journal = {{Physical Review Letters}},
     15958  year = {2002},
     15959  volume = {{89}},
     15960  number = {{6}},
     15961  pages = {{065502}}
     15962}
     15963@article{Watkins2004,
     15964  author = {Watkins, Lucas P. and Yang, Haw},
     15965  title = {{Information Bounsd and Optimal Analysis of Dynamic Single Molecule Measurements}},
     15966  journal = {{Biophysical Journal}},
     15967  year = {2004},
     15968  volume = {{86}},
     15969  number = {{6}},
     15970  pages = {{4015-4029}}
     15971}
     15972@article{Elburg2007,
     15973  author = {Elburg, H.J. van and Kuypers, L.C. and Decraemer, W.F. and Dirckx, J.J.J.},
     15974  title = {{Improved correction of axial geometrical distortion in index-mismatched fluorescent confocal microscopic images using high-aperture objective lenses}},
     15975  journal = {{Journal of Microscopy}},
     15976  year = {2007},
     15977  volume = {{228}},
     15978  number = {{1}},
     15979  pages = {{45-54}}
     15980}
     15981@phdthesis{Li2006,
     15982  author = {Li, Jinyu and Nelson, Philip C. and Betterton, M.D.},
     15983  title = {{DNA entropic elasticity for short molecules attached to beads}},
     15984  year = {2006}
     15985}
     15986@book{Cohen1988,
     15987  author = {Cohen, A. Clifford and Whitten, Betty Jones},
     15988  title = {{Parameter estimation in reliability and life span models}},
     15989  year = {1988},
     15990  volume = {{96}},
     15991  publisher = {{Marcel Dekker, Inc}},
     15992  series = {{Statistics: Textbooks and monographs}},
     15993  address = {{New York}}
     15994}
     15995@article{Cocco2002,
     15996  author = {Cocco, S. and Marko, J.F. and Monasson, R.},
     15997  title = {{Theoretical models for single-molecule DNA and RNA experiments: from elasticity to unzipping}},
     15998  journal = {{Comptes rendus de l'Academie des Sciences Physique}},
     15999  year = {2002},
     16000  volume = {{3}},
     16001  pages = {{569-584}}
     16002}
     16003@article{Cocco2003,
     16004  author = {Cocco, S. and Marko, J.F. and Monasson, R. and Sarkar, A. and Yan, J.},
     16005  title = {{Force-extension behavior of folding polymers}},
     16006  journal = {{The European Physical Journal E}},
     16007  year = {2003},
     16008  volume = {{10}},
     16009  pages = {{249-263}}
     16010}
     16011@article{Hughes2001,
     16012  author = {Hughes, Timothy R. and Shoemaker, Daniel D.},
     16013  title = {{DNA microarrays for expression profiling}},
     16014  journal = {{Current Opinion in Chemical Biology}},
     16015  year = {2001},
     16016  volume = {{5}},
     16017  pages = {{21-25}}
     16018}
     16019@article{Tinland1997,
     16020  author = {Tinland, Bernard and Pluen, Alain and Sturm, Jean and Weill, Gilbert},
     16021  title = {{Persistence Length of Single-Stranded DNA}},
     16022  journal = {{Macromolecules}},
     16023  year = {1997},
     16024  volume = {{30}},
     16025  number = {{19}},
     16026  pages = {{5763-5765}}
     16027}
     16028@article{Massey1951,
     16029  author = {Massey, Frank J., Jr.},
     16030  title = {{The Kolmogorov-Smirnov test for goodness of fit}},
     16031  journal = {{Journal of the American Statistical Association}},
     16032  year = {1951},
     16033  volume = {{46}},
     16034  pages = {{68-78}}
     16035}
     16036@article{Burkhardt1993,
     16037  author = {Burkhardt, Theodore W.},
     16038  title = {{Semiflexible polymer in the half plane and statistics of the integral of a Brownian curve}},
     16039  journal = {{Journal of Physics A: Mathematical and General}},
     16040  year = {1993},
     16041  volume = {{26}},
     16042  pages = {{L1157-L1162}}
     16043}
     16044@article{Stepanow2002,
     16045  author = {Stepanow, S. and Sch\\\"utz, G. M.},
     16046  title = {{The distribution function of a semiflexible polymer and random walks with constraints}},
     16047  journal = {{Europhysics Letters (EPL)}},
     16048  year = {2002},
     16049  volume = {{60}},
     16050  number = {{4}},
     16051  pages = {{546-551}}
     16052}
     16053@article{Smith1992,
     16054  author = {Smith, Steven B. and Finzi, Laura and Bustamante, Carlos},
     16055  title = {{Direct Mechanical Measurement of the Elasticity of Single DNA Molecules by Using Magnetic Beads}},
     16056  journal = {{Science}},
     16057  year = {1992},
     16058  volume = {{258}},
     16059  number = {{5085}},
     16060  pages = {{1122-1126}}
     16061}
     16062@article{Bao2002,
     16063  author = {Bao, Paul and Frutor, Anthony G. and Greef, Charles and Lahiri, Joydeep and Muller, Uwe and Peterson, Todd C. and Warden, Laurence and Xie, Xinying},
     16064  title = {{High-Sensitivity Detection of DNA Hybridization on Microarrays Using Resonance Light Scattering}},
     16065  journal = {{Analytical Chemistry}},
     16066  year = {2002},
     16067  volume = {{74}},
     16068  number = {{8}},
     16069  pages = {{1792-1979}}
     16070}
     16071@article{Baumann1997,
     16072  author = {Baumann, Christoph G. and Smith, Steven B. and Bloomfield, Victor A. and Bustamante, Carlos},
     16073  title = {{Ionic effects on the elasticity of single DNA molecules}},
     16074  journal = {{Proceedings of the National Academy of Sciences of the USA}},
     16075  year = {1997},
     16076  volume = {{94}},
     16077  pages = {{6185-6190}}
     16078}
     16079@article{Vandenberg1991,
     16080  author = {Vandenberg, Elaine T. and Bertilsson, Lars and Liedberg, Bo and Uvdal, Kajsa and Erlandsson, Ragnar and Elwing, Hans and Lundstrom, Ingemar},
     16081  title = {{Structure of 3-aminopropyl triethoxy silane on silicon oxide}},
     16082  journal = {{Journal of Colloid and Interface Science}},
     16083  year = {1991},
     16084  volume = {{147}},
     16085  number = {{1}},
     16086  pages = {{103-118}}
     16087}
     16088@article{Blumberg2005,
     16089  author = {Blumberg, Seth and Gajraj, Arivalagan and Pennington, Matthew W.},
     16090  title = {{Three-Dimensional Characterization of Tethered Microspheres by Total Internal Reflection Fluorescence Microscopy}},
     16091  journal = {{Biophysical Journal}},
     16092  year = {2005},
     16093  volume = {{89}},
     16094  pages = {{1272-1281}}
     16095}
     16096@misc{Neumann2001,
     16097  author = {Neumann, Richard M.},
     16098  title = {{Entropic Elasticity of Weakly Perturbed Polymers}},
     16099  year = {2001},
     16100  pages = {11},
     16101  month = {January 22, 2001},
     16102  publisher = {{The Energy Institute, The Pennsylvania State University}}
     16103}
     16104@article{Ommering2010,
     16105  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.},
     16106  title = {{Mobility and height detection of particle labels in an optical evanescent wave biosensor with single-label resolution}},
     16107  journal = {{Journal of Physics D: Applied Physics}},
     16108  year = {2010},
     16109  volume = {{43}},
     16110  number = {{15}},
     16111  pages = {{155501}}
     16112}
     16113@article{Heaton2001,
     16114  author = {Heaton, Richard J. and Peterson, Alexander W. and Georgiadis, Rosina M.},
     16115  title = {{Electrostatic surface plasmon resonance: Direct electric field-induced hybridization and denaturation in monolayer nucleic acid films and label-free discrimination of base mismatches}},
     16116  journal = {{Proceedings of the National Academy of Sciences of the USA}},
     16117  year = {2001},
     16118  volume = {{98}},
     16119  number = {{7}},
     16120  pages = {{3701-3704}}
     16121}
     16122@article{Gobush1972,
     16123  author = {Gobush, William and Yamakawa, Hiromi and Stockmayer, W. H. and Magee, W. S.},
     16124  title = {{Statistical Mechanics of Wormlike Chains. I. Asymptotic Behavior}},
     16125  journal = {{The Journal of Chemical Physics}},
     16126  year = {1972},
     16127  volume = {{57}},
     16128  number = {{7}},
     16129  pages = {{2839-2843}}
     16130}
     16131@article{Henderson2001,
     16132  author = {Henderson, Michael and Meyer, Mary C.},
     16133  title = {{Exploring the Confidence Interval for a Binomial Parameter in a First Course in Statistical Computing}},
     16134  journal = {{The American Statistician}},
     16135  year = {2001},
     16136  volume = {{55}},
     16137  number = {{4}},
     16138  pages = {{337-344}}
     16139}
     16140@article{Winkler1994,
     16141  author = {Winkler, Roland G. and Reineker, Peter and Harnau, Ludger},
     16142  title = {{Models and equilibrium properties of stiff molecular chains}},
     16143  journal = {{journal of Chemical Physics}},
     16144  year = {1994},
     16145  volume = {{101}},
     16146  number = {{9}},
     16147  pages = {{8119-8129}}
     16148}
     16149@article{William1972,
     16150  author = {William, Gobush and Hiromi, Yamakawa and Stockmayer, W. H. and Magee, W. S.},
     16151  title = {{Statistical Mechanics of Wormlike Chains. I. Asymptotic Behavior}},
     16152  journal = {{The Journal of Chemical Physics}},
     16153  year = {1972},
     16154  volume = {{57}},
     16155  number = {{7}},
     16156  pages = {{2839-2843}}
     16157}
     16158@article{Peterlinz1997,
     16159  author = {Peterlinz, Kevin A. and Georgiadis, Rosina M. and Herne, Tonya M. and Tarlov, Michael J.},
     16160  title = {{Observation of Hybridization and Dehybridization of Thiol-Tethered DNA Using Two-Color Surface Plasmon Resonance Spectroscopy}},
     16161  journal = {{Journal of the American Chemical Society}},
     16162  year = {1997},
     16163  volume = {{119}},
     16164  pages = {{3401-3402}}
     16165}
     16166@article{Morriss2010,
     16167  author = {Morriss-Andrews, Alex and Rottler, Joerg and Plotkin, Steven S.},
     16168  title = {{A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality}},
     16169  journal = {{The Journal of Chemical Physics}},
     16170  year = {2010},
     16171  volume = {{132}},
     16172  number = {{3}},
     16173  pages = {{035105}}
     16174}
     16175@article{Chandrasekhar1943,
     16176  author = {Chandrasekhar, S.},
     16177  title = {{Stochastic Problems in Physics and Astronomy}},
     16178  journal = {{Revieuws of Modern Physics}},
     16179  year = {1943},
     16180  volume = {{15}},
     16181  number = {{1}},
     16182  pages = {{2-87}}
     16183}
     16184@inproceedings{Ram2005,
     16185  author = {Ram, Sripad and Ward, E. Sally and Ober, Raimond J.},
     16186  title = {{How accurately can a single molecule be localized in three dimensions using a fluorescence microscope?}},
     16187  year = {2005},
     16188  volume = {{5699}},
     16189  pages = {426-435},
     16190  series = {{Proceedings of SPIE}},
     16191  booktitle = {{Imaging, Manipulation and Analysis of Biomolecule and Cells: Fundamentals and Applications III}}
     16192}
     16193@book{Papoulis1991,
     16194  author = {Papoulis, Athanasios},
     16195  title = {{Probability, random variables, and stochastic processes}},
     16196  year = {1991},
     16197  publisher = {{McGraw-Hill}},
     16198  series = {{McGraw-Hill series in electrical engineering, Communications and signal processing}},
     16199  address = {{Singapore}},
     16200  edition = {{Third edition}}
     16201}
     16202@inproceedings{Ram2007,
     16203  author = {Ram, Sripad and Chao, Jerry and Prabhat, Prashant and Ward, E. Sally and Ober, Raimond J.},
     16204  title = {{A novel approach to determining the three-dimensional location of microscopic objects with applications to 3D particle tracking}},
     16205  year = {2007},
     16206  volume = {{6443}},
     16207  pages = {64430D},
     16208  editor = {Conchello, Jose-Angel and Cogswell, Carol J. and Wilson, Tony},
     16209  publisher = {{Proceedings of SPIE}},
     16210  booktitle = {{Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XIV}}
     16211}
     16212@article{Wu2005,
     16213  author = {Wu, Mingming and Roberts, John W. and Buckley, Mark},
     16214  title = {{Three-dimensional fluorescent particle tracking at micron-scale using a single camera}},
     16215  journal = {{Experiments in Fluids}},
     16216  year = {2005},
     16217  volume = {{38}},
     16218  pages = {{461-465}}
     16219}
     16220@article{Maier2000,
     16221  author = {Maier, Berenike and Bensimon, David and Croquette, Vincent},
     16222  title = {{Replication by a single DNA polymerase of a stretched single-stranded DNA}},
     16223  journal = {{Proceedings of the National Academy of Sciences of the USA}},
     16224  year = {2000},
     16225  volume = {{97}},
     16226  number = {{22}},
     16227  pages = {{12002-12007}}
     16228}
     16229@misc{Odijk2005,
     16230  author = {Odijk, Theo},
     16231  title = {{Note on DNA grafted to a surface (experiments Heidi Dietrich, TU Delft)}},
     16232  year = {2005},
     16233  month = {August 4, 2005}
     16234}
     16235@article{Zimm1956,
     16236  author = {Zimm, Bruno H.},
     16237  title = {{Dynamics of Polymer Molecules in Dilute Solution: Viscoelasticity, Flow Birefringence and Dielectric Loss}},
     16238  journal = {{The Journal of Chemical Physics}},
     16239  year = {1956},
     16240  volume = {{24}},
     16241  number = {{2}},
     16242  pages = {{269-278}}
     16243}
     16244@article{Sadr2007,
     16245  author = {Sadr, Reza and Hohenegger, Christel and Li, Haifeng and Mucha, Peter J. and Yoda, Minami},
     16246  title = {{Diffusion-induced bias in near-wall velocimetry}},
     16247  journal = {{Journal of Fluid Mechanics}},
     16248  year = {2007},
     16249  volume = {{577}},
     16250  pages = {{443-456}}
     16251}
     16252@article{Qian2000b,
     16253  author = {Qian, Hong},
     16254  title = {{Single-Particle Tracking: Brownian Dynamics of Viscoelastic Materials}},
     16255  journal = {{Biophysical Journal}},
     16256  year = {2000},
     16257  volume = {{79}},
     16258  number = {{1}},
     16259  pages = {{137-143}}
     16260}
     16261@article{Pirrung2002,
     16262  author = {Pirrung, Michael C.},
     16263  title = {{How to Make a DNA Chip}},
     16264  journal = {{Angewandte Chemie International Edition}},
     16265  year = {2002},
     16266  volume = {{41}},
     16267  number = {{8}},
     16268  pages = {{1276-1289}}
     16269}
     16270@article{Marko2003,
     16271  author = {Marko, John F. and Cocco, Simona},
     16272  title = {{The micromechanics of DNA}},
     16273  journal = {{Physics World}},
     16274  year = {2003},
     16275  volume = {{16}},
     16276  number = {{3}}
     16277}
     16278@article{Qian2000a,
     16279  author = {Qian, Hong},
     16280  title = {{A mathematical analysis for the Brownian dynamics of a DNA tether}},
     16281  journal = {{Journal of Mathematical Biology}},
     16282  year = {2000},
     16283  volume = {{41}},
     16284  number = {{4}},
     16285  pages = {{331-340}}
     16286}
     16287@misc{Marko2005,
     16288  author = {Marko, J.F.},
     16289  title = {{Introduction to Single-DNA Micromechanics}},
     16290  year = {2005},
     16291  pages = {63},
     16292  month = {June 2, 2005},
     16293  publisher = {{Department of Physics, University of Illinois at Chicago}}
     16294}
     16295@article{Schaefer1980,
     16296  author = {Schaefer, D.W. and Joanny, J.F. and Pincus, P.},
     16297  title = {{Dynamics of Semiflexible Polymers in Solution}},
     16298  journal = {{Macromolecules}},
     16299  year = {1980},
     16300  volume = {{13}},
     16301  number = {{5}},
     16302  pages = {{1280-1289}}
     16303}
     16304@article{Zurla2006,
     16305  author = {Zurla, C. and Franzini, A. and Galli, G. and Dunlap, D. D. and Lewis, D. E. A. and Adhya, S. and Finzi, L.},
     16306  title = {{Novel tethered particle motion analysis of CI protein-mediated DNA looping in the regulation of bacteriophage lambda}},
     16307  journal = {{Journal of Physics: Condensed Matter}},
     16308  year = {2006},
     16309  volume = {{18}},
     16310  pages = {{S225-S234}}
     16311}
     16312@article{Prabhat2007,
     16313  author = {Prabhat, Prashant and Gan, Zhuo and Chao, Jerry and Ram, Sripad and Vaccaro, Carlos and Gibbons, Steven and Ober, Raimond J. and Ward, E. Sally},
     16314  title = {{Elucidation of intracellular recycling pathways leading to exocytosis of the Fc receptor, FcRn, by using multifocal plane microscopy}},
     16315  journal = {{Proceedings of the National Academy of Sciences of the USA}},
     16316  year = {2007},
     16317  volume = {{104}},
     16318  number = {{14}},
     16319  pages = {{5889-5894}}
     16320}
     16321@inproceedings{Prabhat2006,
     16322  author = {Prabhat, Prashant and Ram, Sripad and Ward, E. Sally and Ober, Raimond J.},
     16323  title = {{Simultaneous imaging of several focal planes in fluorescence microscopy for the study of cellular dynamics in 3D}},
     16324  year = {2006},
     16325  volume = {{6090}},
     16326  pages = {60900L},
     16327  editor = {Conchello, Jose-Angel and Cogswell, Carol J. and Wilson, Tony},
     16328  publisher = {{Proceedings of SPIE}},
     16329  booktitle = {{Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XIII}}
     16330}
     16331@article{Marko1994,
     16332  author = {Marko, John F. and Siggia, Eric D.},
     16333  title = {{Fluctuations and Supercoiling of DNA}},
     16334  journal = {{Science}},
     16335  year = {1994},
     16336  volume = {{265}},
     16337  number = {{5171}},
     16338  pages = {{506-508}}
     16339}
     16340@article{Marko1995,
     16341  author = {Marko, John F. and Siggia, Eric D.},
     16342  title = {{Stretching DNA}},
     16343  journal = {{Macromolecules}},
     16344  year = {1995},
     16345  volume = {{28}},
     16346  number = {{26}},
     16347  pages = {{8759-8770}}
     16348}
     16349@article{Winkler1992,
     16350  author = {Winkler, R.G. and Reineker, P.},
     16351  title = {{Finitie Size Distribution and Partition Functions of Gaussian Chains: Maximum Entropy Approach}},
     16352  journal = {{Macromolecules}},
     16353  year = {1992},
     16354  volume = {{25}},
     16355  number = {{24}},
     16356  pages = {{6891-6896}}
     16357}
     16358@article{Berciaud2005,
     16359  author = {Berciaud, St\\\'ephane and Cognet, Laurent and Tamarat, Philippe and Lounis, Brahim},
     16360  title = {{Observation of Intrinsic Size Effects in the Optical Response of Individual Gold Nanoparticles}},
     16361  journal = {{Nano Letters}},
     16362  year = {2005},
     16363  volume = {{5}},
     16364  number = {{3}},
     16365  pages = {{515-518}}
     16366}
     16367@article{Lahtinen2001,
     16368  author = {Lahtinen, J.M. and Hjelt, T. and Ala-Nissila, T. and Chvoj, Z.},
     16369  title = {{Diffusion of hard disks and rodlike molecules on surfaces}},
     16370  journal = {{Physical Review E}},
     16371  year = {2001},
     16372  volume = {{64}}
     16373}
     16374@article{Wong2006,
     16375  author = {Wong, Wesley P. and Halvorsen, Ken},
     16376  title = {{The effect of integration time on fluctuation measurements: calibrating an optical trap in the presence of motion blur}},
     16377  journal = {{Optics Express}},
     16378  year = {2006},
     16379  volume = {{14}},
     16380  number = {{25}},
     16381  pages = {{12517-12531}}
     16382}
     16383@article{Perkins1994,
     16384  author = {Perkins, Thomas T. and Quake, Stephern R. and Smith, Douglas E. and Chu, Steven},
     16385  title = {{Relaxation of a Single DNA Molecule Observed by Optical Microscopy}},
     16386  journal = {{Science}},
     16387  year = {1994},
     16388  volume = {{264}},
     16389  pages = {{822-826}}
     16390}
     16391@article{Lu2002,
     16392  author = {Lu, Yongjun and Weers, Brock and Stellwagen, Nancy C.},
     16393  title = {{DNA Persistencde Length Revisited}},
     16394  journal = {{Biopolymers}},
     16395  year = {2002},
     16396  volume = {{61}},
     16397  pages = {{261-275}}
     16398}
     16399@article{Laurens2009,
     16400  author = {Laurens, Niels and Bellamy, Stuart R. W. and Harms, August F. and Kovacheva, Yana S. and Halford, Stephen F. and Wuite, Gijs J. L.},
     16401  title = {{Dissecting protein-induced DNA looping dynamics in real time}},
     16402  journal = {{Nucleic Acids Research}},
     16403  year = {2009}
     16404}
     16405@article{Yguerabide1998b,
     16406  author = {Yguerabide, Juan and Yguerabide, Evangelina E.},
     16407  title = {{Light-Scattering Submicroscopic Particles as Highly Fluorescent Analogs and Their Use as Tracer Labels in Clinical and Biological Applications. II. Experimental Characterization}},
     16408  journal = {{Analytical Biochemistry}},
     16409  year = {1998},
     16410  volume = {{262}},
     16411  pages = {{157-176}}
     16412}
     16413@article{Capitanio2004,
     16414  author = {Capitanio, M. and Vanzi, F. and Broggio, C. and Cicchi, R. and Normanno, D. and Romano, G. and Sacconi, L. and Pavone, F.S.},
     16415  title = {{Exploring Molecular Motors and Switches at the Single-Molecule Level}},
     16416  journal = {{Microscopy Research and Technique}},
     16417  year = {2004},
     16418  volume = {{65}},
     16419  pages = {{194-204}}
     16420}
     16421@article{Sheppard2004,
     16422  author = {Sheppard, Colin J.R.},
     16423  title = {{Annular pupils, radial polarization, and superresolution}},
     16424  journal = {{Applied Optics}},
     16425  year = {2004},
     16426  volume = {{43}},
     16427  number = {{22}},
     16428  pages = {{4322-4327}}
     16429}
     16430@article{Zhu2006,
     16431  author = {Zhu, Qiang and Zeng, Jun and Triantafyllou, Michael S. and Yue, Dick K.P.},
     16432  title = {{Direct Numerical Simulation of Single-Molecule DNA by Cable Dynamics}},
     16433  journal = {{Journal of Microelectromechanical Systems}},
     16434  year = {2006},
     16435  volume = {{15}},
     16436  number = {{5}},
     16437  pages = {{1078-1087}}
     16438}
     16439@article{Strick1998,
     16440  author = {Strick, T.R. and Allemand, J.-F. and Bensimon, D. and Croquette, V.},
     16441  title = {{Behavior of Supercoiled DNA}},
     16442  journal = {{Biophysical Journal}},
     16443  year = {1998},
     16444  volume = {{74}},
     16445  pages = {{2016-2028}}
     16446}
     16447@article{Pouget2004,
     16448  author = {Pouget, Noelle and Dennis, Cynthia and Turlan, Catherine and Grigoriev, Mikhail and Chandler, Michael and Salome, Laurence},
     16449  title = {{Single-particle tracking for DNA tether length monitoring}},
     16450  journal = {{Nucleic Acids Research}},
     16451  year = {2004},
     16452  volume = {{32}},
     16453  number = {{9}}
     16454}
     16455@article{Saito1967,
     16456  author = {Saito, Nobuhiko and Takahashi, Kunihiko and Yunoki, Yasuo},
     16457  title = {{The Statistical Mechanical Theory of Stiff Chains}},
     16458  journal = {{Journal of the Physical Society of Japan}},
     16459  year = {1967},
     16460  volume = {{22}},
     16461  number = {{1}},
     16462  pages = {{219-226}}
     16463}
     16464@article{Smith1996,
     16465  author = {Smith, Steven B. and Cui, Yujia and Bustamante, Carlos},
     16466  title = {{Overstretching B-DNA: The Elastic Response of Individual Double-Stranded and Single-Stranded DNA Molecules}},
     16467  journal = {{Science}},
     16468  year = {1996},
     16469  volume = {{271}},
     16470  number = {{5250}},
     16471  pages = {{795-799}}
     16472}
     16473@article{Roeffaers2007,
     16474  author = {Roeffaers, Maarten B.J. and De Cremer, Gert and Uji-i, Hiroshi and Muls, Beniot and Sels, Bert F. and Jacobs, Pierre A. and De Schryver, Frans C. and De Vos, Dirk E. and Hofkens, Johan},
     16475  title = {{Single-molecule fluorescence spectroscopy in (bio)catalysis}},
     16476  journal = {{Proceedings of the National Academy of Sciences of the USA}},
     16477  year = {2007},
     16478  volume = {{104}},
     16479  number = {{31}},
     16480  pages = {{12603-12609}}
     16481}
     16482@book{Pluta1989,
     16483  author = {Pluta, Maksymilian},
     16484  title = {{Advanced Light Microscopy}},
     16485  year = {1989},
     16486  volume = {{2: Specialized Methods}},
     16487  publisher = {{Elsevier}},
     16488  address = {{Amsterdam}}
     16489}
     16490@book{Pluta1988,
     16491  author = {Pluta, Maksymilian},
     16492  title = {{Advanced Light Microscopy}},
     16493  year = {1988},
     16494  volume = {{1: Principles and Basic Properties}},
     16495  publisher = {{Elsevier}},
     16496  address = {{Amsterdam}}
     16497}
     16498@article{Broek2006,
     16499  author = {Broek, Bram van den and Vanzi, Francesco and Normanno, Davide and Pavone, Francesco S. and Wuite, Gijs J. L.},
     16500  title = {{Real-time observation of DNA looping dynamics of Type IIE restriction enzymes NaeI and NarI}},
     16501  journal = {{Nucleic Acids Research}},
     16502  year = {2006},
     16503  volume = {{34}},
     16504  number = {{1}},
     16505  pages = {{167-174}}
     16506}
     16507@article{Braslavsky2003,
     16508  author = {Braslavsky, Ido and Hebert, Benedict and Kartalov, Emil and Quake, Stephern R.},
     16509  title = {{Sequence Information can be Obtained from Single DNA Molecules}},
     16510  journal = {{Proceedings of the National Academy of Sciences of the USA}},
     16511  year = {2003},
     16512  volume = {{100}},
     16513  number = {{7}},
     16514  pages = {{3960-3964}}
     16515}
     16516@article{Ariel2003,
     16517  author = {Ariel, Gil and Andelman, David},
     16518  title = {{Persistence length of a strongly charged rodlike polyelectrolyte in the presence of salt}},
     16519  journal = {{Physical Review E}},
     16520  year = {2003},
     16521  volume = {{67}},
     16522  number = {{1}},
     16523  pages = {{011805-1-011805-11}}
     16524}
     16525@article{Yamakawa1972,
     16526  author = {Yamakawa, Hiromi and Stockmayer, W. H.},
     16527  title = {{Statistical Mechanics of Wormlike Chains. II. Excluded Volume Effects}},
     16528  journal = {{The Journal of Chemical Physics}},
     16529  year = {1972},
     16530  volume = {{57}},
     16531  number = {{7}},
     16532  pages = {{2843-2854}}
     16533}
     16534@article{Davidson1995,
     16535  author = {Davidson, John A.},
     16536  title = {{Arrays of Uniform Latex Spheres as Test Objects in Optical Microscopy}},
     16537  journal = {{Particle and Particle Systems Characterization}},
     16538  year = {1995},
     16539  volume = {{12}},
     16540  pages = {{173-178}}
     16541}
     16542@article{Huisken2004,
     16543  author = {Huisken, Jan and Swoger, Jim and Del Bene, Filippo and Wittbrodt, Joachim and Stelzer, Ernst H. K.},
     16544  title = {{Optical Sectioning Deep Inside Live Embryos by Selective Plane Illumination Microscopy}},
     16545  journal = {{Science}},
     16546  year = {2004},
     16547  volume = {{305}},
     16548  number = {{5686}},
     16549  pages = {{1007-1009}}
     16550}
     16551@article{Goldman1967,
     16552  author = {Goldman, A.J. and Cox, R.G. and Brenner, H.},
     16553  title = {{Slow viscous motion of a sphere parallel to a plane wall - I Motion through a quiescent fluid}},
     16554  journal = {{Chemical Engineering Science}},
     16555  year = {1967},
     16556  volume = {{22}},
     16557  number = {{4}},
     16558  pages = {{637-651}}
     16559}
     16560@article{Maher2007,
     16561  author = {Maher, Brendan},
     16562  title = {{Spring theory}},
     16563  journal = {{Nature}},
     16564  year = {2007},
     16565  volume = {{448}},
     16566  pages = {{984-986}}
     16567}
     16568@article{Cui2008,
     16569  author = {Cui, Xiquan and Lee, Lap Man and Heng, Xin and Zhong, Weiwei and Sternberg, Paul W. and Psaltis, Demetri and Yang, Changhuei},
     16570  title = {{Lensless high-resolution on-chip optrofluidic microscopes for Caenorhabditis elegans and cell imaging}},
     16571  journal = {{Proceedings of the National Academy of Sciences of the USA}},
     16572  year = {2008},
     16573  volume = {{105}},
     16574  number = {{31}},
     16575  pages = {{10670-10675}}
     16576}
     16577@article{Hagerman1988,
     16578  author = {Hagerman, P.J.},
     16579  title = {{Flexibility of DNA}},
     16580  journal = {{Annual Review of Biophysics and BioEngineering}},
     16581  year = {1988},
     16582  volume = {{17}},
     16583  pages = {{265-286}}
     16584}
     16585@article{Vanzi2006,
     16586  author = {Vanzi, Francesco and Broggio, Chiara and Sacconi, Leonardo and Pavone, Francesco Saverio},
     16587  title = {{Lac repressor hinge flexibility and DNA looping: single molecule kinetics by tethered particle motion}},
     16588  journal = {{Nucleic Acids Research}},
     16589  year = {2006},
     16590  volume = {{34}},
     16591  number = {{12}},
     16592  pages = {{3409-3420}}
     16593}
     16594@article{Bronstein2009,
     16595  author = {Bronstein, I. and Israel, Y. and Kepten, E. and Mai, S. and Shav-Tal, Y. and Barkai, E. and Garini, Y.},
     16596  title = {{Transient Anomalous Diffusion of Telomeres in the Nucleus of Mammalian Cells}},
     16597  journal = {{Physical Review Letters}},
     16598  year = {2009},
     16599  volume = {{103}},
     16600  number = {{1}},
     16601  pages = {{018102}}
     16602}
     16603@article{Bawendi1985,
     16604  author = {Bawendi, M.G. and Freed, Karl F.},
     16605  title = {{A Wiener integral model for stiff polymer chains}},
     16606  journal = {{Journal of Chemical Physics}},
     16607  year = {1985},
     16608  volume = {{83}},
     16609  number = {{5}},
     16610  pages = {{2491}}
     16611}
     16612@article{Martin2002,
     16613  author = {Martin, Douglas S. and Forstner, Martin B. and K\\\"as, Josef A.},
     16614  title = {{Apparent Subdiffusion Inherent to Single Particle Tracking}},
     16615  journal = {{Biophysical Journal}},
     16616  year = {2002},
     16617  volume = {{83}},
     16618  number = {{4}},
     16619  pages = {{2109-2117}}
     16620}
     16621@article{Savelkoul2006,
     16622  author = {Savelkoul, Paul H.M. and Catsburg, Arnold and Mulder, Sije and Oostendorp, Ludo and Schirm, Jurjen and Wilke, Hans and van der Zanden, Adri G.M. and Noordhoek, Gerda T.},
     16623  title = {{Detection of Mycobacterium tuberculosis complex with Real Time PCR: Comparison of different primer-probe sets based on the IS6110 element}},
     16624  journal = {{Journal of Microbiological Methods}},
     16625  year = {2006},
     16626  volume = {{66}},
     16627  number = {{1}},
     16628  pages = {{177-180}}
     16629}
     16630@article{Bustamante2000,
     16631  author = {Bustamante, Carlos and Smith, Steven B. and Liphardt, Jan and Smith, Doug},
     16632  title = {{Single-molecule studies of DNA mechanics}},
     16633  journal = {{Current Opinion in Structural Biology}},
     16634  year = {2000},
     16635  volume = {{10}},
     16636  number = {{3}},
     16637  pages = {{279-285}}
     16638}
     16639@article{Bustamante2003,
     16640  author = {Bustamante, Carlos and Bryant, Zev and Smith, Steven B.},
     16641  title = {{Ten years of tension: single-molecule DNA mechanics}},
     16642  journal = {{Nature}},
     16643  year = {2003},
     16644  volume = {{421}},
     16645  pages = {{423-427}}
     16646}
     16647@article{Holtzer2007,
     16648  author = {Holtzer, Laurent and Meckel, Tobias and Schmidt, Thomas},
     16649  title = {{Nanometric three-dimensional tracking of individual quantom dots in cells}},
     16650  journal = {{Applied Physics Letters}},
     16651  year = {2007},
     16652  volume = {{90}},
     16653  pages = {{053902}}
     16654}
     16655@article{Huang2008,
     16656  author = {Huang, Bo and Wang, Wenqin and Bates, Mark and Zhuang, Xiaowei},
     16657  title = {{Three-Dimensional Super-Resolution Imaging by Stochastic Optical Reconstruction Microscopy}},
     16658  journal = {{Science}},
     16659  year = {2008},
     16660  volume = {{319}},
     16661  pages = {{810-813}}
     16662}
     16663@article{Lindner2009,
     16664  author = {Lindner, Moshe and Nir, Guy and Dietrich, Heidelinde R. C. and Young, Ian T. and Tauber, Elad and Bronshtein, I. and Altman, Liat and Garini, Yuval},
     16665  title = {{Studies of Single Molecules in their Natural Form}},
     16666  journal = {{Israel Journal of Chemistry}},
     16667  year = {2009},
     16668  volume = {{49}},
     16669  pages = {{283-291}}
     16670}
     16671@article{Wilhelm1996,
     16672  author = {Wilhelm, Jan and Frey, Erwin},
     16673  title = {{Radial Distribution Function of Semiflexible Polymers}},
     16674  journal = {{Physical Review Letters}},
     16675  year = {1996},
     16676  volume = {{77}},
     16677  number = {{12}},
     16678  pages = {{2581}}
     16679}
     16680@article{Clercx1992,
     16681  author = {Clercx, H.J.H. and Schram, P.P.J.M.},
     16682  title = {{Brownian particles in shear flow and harmonic potentials: A study of long-time tails}},
     16683  journal = {{Physical Review A}},
     16684  year = {1992},
     16685  volume = {{46}},
     16686  number = {{4}},
     16687  pages = {{1942-1950}}
     16688}
     16689@inproceedings{Subotic2004,
     16690  author = {Subotic, Nadja and van de Ville, Dimitri and Unser, Michael},
     16691  title = {{On the Feasability of Axial Tracking of a Fluorescent Nano-Particle Using a Defocusing Model}},
     16692  year = {2004},
     16693  volume = {{2}},
     16694  pages = {1231-1234},
     16695  booktitle = {{Proceedings IEEE International Symposium on Biomedical Imaging: From Macro to Nano}}
     16696}
     16697@article{Ebenstein2009,
     16698  author = {Ebenstein, Yuval and Gassman, Natalie and Kim, Soohong and Antelman, Josh and Kim, Younggyu and Ho, Sam and Samuel, Robin and Michalet, Xavier and Weiss, Shimon},
     16699  title = {{Lighting Up Individual DNA Binding Proteins with Quantum Dots}},
     16700  journal = {{Nano Letters}},
     16701  year = {2009},
     16702  volume = {{9}},
     16703  number = {{4}},
     16704  pages = {{1598-1603}}
     16705}
     16706@article{Harlepp2004,
     16707  author = {Harlepp, S. and Robert, J. and Darnton, N.C. and Chateney, D.},
     16708  title = {{Subnanometric measurements of evanescent wave penetration depth using total internal reflection microscopy combined with fluorescent correlation spectroscopy}},
     16709  journal = {{Applied Physics Letters}},
     16710  year = {2004},
     16711  volume = {{85}},
     16712  number = {{17}}
     16713}
     16714@inproceedings{Nguyen2000,
     16715  author = {Nguyen, Lam K. and Bravo-Zanoguera, Miguel and Kellner, Albert L. and Price, Jeffrey H.},
     16716  title = {{Magnification Corrected Optical Image Splitting for Simultaneous Multiplanar Acquisition}},
     16717  year = {2000},
     16718  volume = {{3921}},
     16719  pages = {31-40},
     16720  editor = {Farkas, Daniel L. and Leif, Robert C.},
     16721  publisher = {{Proceedings of SPIE}},
     16722  booktitle = {{Optical Diagnostics of Living Cells III}}
     16723}
     16724@article{Baslavsky2001,
     16725  author = {Baslavsky, Ido and Amit, Roee and Jaffar Ali, B.M. and Gileadi, Opher and Oppenheim, Amos and Stavans, Joel},
     16726  title = {{Objective-type dark-field illumination for scattering from microbeads}},
     16727  journal = {{Applied Optics}},
     16728  year = {2001},
     16729  volume = {{40}},
     16730  number = {{31}},
     16731  pages = {{5650-5667}}
     16732}
     16733@article{Stepanow2004,
     16734  author = {Stepanow, S.},
     16735  title = {{Statistical mechanics of semiflexible polymers}},
     16736  journal = {{The European Physical Journal B}},
     16737  year = {2004},
     16738  volume = {{39}},
     16739  number = {{4}},
     16740  pages = {{499-512}}
     16741}
     16742@article{Gelles1988,
     16743  author = {Gelles, Jeff and Schnapp, Bruce J. and Sheetz, Michael P.},
     16744  title = {{Tracking kinesin-driven movements with nanometric-scale precision}},
     16745  journal = {{Nature}},
     16746  year = {1988},
     16747  volume = {{331}},
     16748  number = {{6155}},
     16749  pages = {{450-453}}
     16750}
     16751@book{Rubinstein2006,
     16752  author = {Rubinstein, Michael and Colby, Ralph H.},
     16753  title = {{Polymer Physics}},
     16754  year = {2006},
     16755  publisher = {{Oxford University Press Inc.}},
     16756  address = {{New York}}
     16757}
     16758@article{Seol2007,
     16759  author = {Seol, Yeonee and Li, Jinyu and Nelson, Philip C. and Perkins, Thomas T. and Betterton, M.D.},
     16760  title = {{Elasticity of Short DNA Molecules: Theory and Experiment for Contour Lengths of 0.6-7 um}},
     16761  journal = {{Biophysical Journal}},
     16762  year = {2007},
     16763  volume = {{93}},
     16764  number = {{12}},
     16765  pages = {{4360-4373}}
     16766}
     16767@article{Cohen2007,
     16768  author = {Cohen, Adam E. and Moerner, W.E.},
     16769  title = {{Principle-component analysis of shape fluctuations of single DNA molecules}},
     16770  journal = {{Proceedings of the National Academy of Sciences of the USA}},
     16771  year = {2007},
     16772  volume = {{104}},
     16773  number = {{31}},
     16774  pages = {{12622-12627}}
     16775}
     16776@article{Saxton2007,
     16777  author = {Saxton, Michael J.},
     16778  title = {{A Biological Interpretation of Transient Anomalous Subdiffusion. I. Qualitative Model}},
     16779  journal = {{Biophysical Journal}},
     16780  year = {2007},
     16781  volume = {{92}},
     16782  number = {{4}},
     16783  pages = {{1178-1191}}
     16784}
     16785@article{Otto1994,
     16786  author = {Otto, Matthias and Eckert, Jochen and Vilgis, Thomas A.},
     16787  title = {{Persistence lengths of semiflexible chains - Methods and approximations}},
     16788  journal = {{Macromolecular Theory and Simulations}},
     16789  year = {1994},
     16790  volume = {{3}},
     16791  number = {{3}},
     16792  pages = {{543-555}}
     16793}
     16794@article{Vennemann2007,
     16795  author = {Vennemann, Peter and Lindken, Ralph and Westerweel, Jerry},
     16796  title = {{In vivo whole-field blood velocity measurement techniques}},
     16797  journal = {{Experiments in Fluids}},
     16798  year = {2007},
     16799  volume = {{42}},
     16800  number = {{3}},
     16801  pages = {{495-511}}
     16802}
     16803@article{Vosch2007,
     16804  author = {Vosch, Tom and Antoku, Yasuko and Hsiang, Jung-Cheng and Richards, Chris I. and Gonzalez, Jose I. and Dickson, Robert M.},
     16805  title = {{Strongly emissive individual DNA-encapsulated Ag nanoclusters as single-molecule fluorophores}},
     16806  journal = {{Proceedings of the National Academy of Sciences of the USA}},
     16807  year = {2007},
     16808  volume = {{104}},
     16809  number = {{31}},
     16810  pages = {{12616-12621}}
     16811}
     16812@article{Galletto2006,
     16813  author = {Galletto, Roberto and Amitani, Ichiro and Baskin, Ronald J. and Kowalczykowski, Stephen C.},
     16814  title = {{Direct observation of individual RecA filaments assembling on single DNA molecules}},
     16815  journal = {{Nature}},
     16816  year = {2006},
     16817  volume = {{443}},
     16818  number = {{7113}},
     16819  pages = {{875-878}}
     16820}
     16821@article{Singh-Zocchi2003,
     16822  author = {Singh-Zocchi, Mukta and Dixit, Sanhita and Ivanov, Vassili and Zocchi, Giovanni},
     16823  title = {{Single-molecule detection of DNA hybridization}},
     16824  journal = {{Proceedings of the National Academy of Sciences of the USA}},
     16825  year = {2003},
     16826  volume = {{100}},
     16827  number = {{13}},
     16828  pages = {{7605-7610}}
     16829}
     16830@article{Frej1993,
     16831  author = {Frej, Nasser A. and Prieve, Dennis C.},
     16832  title = {{Hindered diffusion of a single sphere very near a wall in a nonuniform force field}},
     16833  journal = {{Journal of Chemical Physics}},
     16834  year = {1993},
     16835  volume = {{98}},
     16836  number = {{9}},
     16837  pages = {{7552-7564}}
     16838}
     16839@article{Lagowski1991,
     16840  author = {Lagowski, Jolanta B. and Noolandi, Jaan and Nickel, Bernie},
     16841  title = {{Stiff chain model-functional integral approach}},
     16842  journal = {{Journal of Chemical Physics}},
     16843  year = {1991},
     16844  volume = {{95}},
     16845  number = {{2}},
     16846  pages = {{1266-1296}}
     16847}
     16848@article{Bednar1995,
     16849  author = {Bednar, Jan and Furrer, Patrick and Katritch, Vsevolod and Stasiak, Alicja Z. and Dubochet, Jacques and Stasiak, Andrzej},
     16850  title = {{Determination of DNA Persistence Length by Cryo-electron Microscopy. Separation of the Static and Dynamic Contributions to the Apparent Persistence Length of DNA}},
     16851  journal = {{Journal of Molecular Biology}},
     16852  year = {1995},
     16853  volume = {{254}},
     16854  number = {{4}},
     16855  pages = {{579-594}}
     16856}
     16857@article{McIntosh2009,
     16858  author = {McIntosh, D.B. and Ribeck, N. and Saleh, O.A.},
     16859  title = {{Detailed scaling analysis of low-force polyelectrolyte elasticity}},
     16860  journal = {{Physical Review E}},
     16861  year = {2009},
     16862  volume = {{80}},
     16863  number = {{4}},
     16864  pages = {{041803}}
     16865}
     16866@article{Hyeon2006b,
     16867  author = {Hyeon, Changbong and Dima, Ruxandra I. and Thirumalai, D.},
     16868  title = {{Size, shape, and flexibility of RNA structures}},
     16869  journal = {{The Journal of Chemical Physics}},
     16870  year = {2006},
     16871  volume = {{125}},
     16872  number = {{3}},
     16873  pages = {{194905}}
     16874}
     16875@article{Caarls2010,
     16876  author = {Caarls, W. and Rieger, B and de Vries, A.H.B. and Arndt-Jovin, D.J. and Jovin, T.M.},
     16877  title = {{Minimizing light exposure with the programmable array microscope}},
     16878  journal = {{Journal of Microscopy}},
     16879  year = {2010}
     16880}
     16881@article{Jacobsen2006,
     16882  author = {Jacobsen, Volker and Stoller, Patrick and Brunner, Christian and Vogel, Viola and Sandoghdar, Vahid},
     16883  title = {{Interferometric optical detection and tracking of very small gold nanoparticles at a water-glass interface}},
     16884  journal = {{Optics Express}},
     16885  year = {2006},
     16886  volume = {{14}},
     16887  number = {{1}},
     16888  pages = {{405}}
     16889}
     16890@article{Crut2007,
     16891  author = {Cut, Aur\\\'elien and Koster, Daniel A. and Seidel, Ralf and Wiggins, Chris H. and Dekker, Nynke H.},
     16892  title = {{Fast dynamics of supercoiled DNA revealed by single-molecule experiments}},
     16893  journal = {{Proceedings of the National Academy of Sciences of the USA}},
     16894  year = {2007},
     16895  volume = {{104}},
     16896  number = {{29}},
     16897  pages = {{11957-11962}}
     16898}
     16899@article{Yguerabide1998a,
     16900  author = {Yguerabide, Juan and Yguerabide, Evangelina E.},
     16901  title = {{Light-Scattering Submicroscopic Particles as Highly Fluorescent Analogs and Their Use as Tracer Labels in Clinical and Biological Applications. I. Theory}},
     16902  journal = {{Analytical Biochemistry}},
     16903  year = {1998},
     16904  volume = {{262}},
     16905  pages = {{137-156
     16906 }}
     16907}
     16908@article{Strick1998b,
     16909  author = {Strick, T.R. and Allemand, J.-F. and Croquette, V. and Bensimon, D.},
     16910  title = {{Physical Approaches to the Study of DNA}},
     16911  journal = {{Journal of Statistical Physics}},
     16912  year = {1998},
     16913  volume = {{93}},
     16914  number = {{3-4}},
     16915  pages = {{647-672}}
     16916}
     16917@article{Rechendorff2009,
     16918  author = {Rechendorff, Kristian and Witz, Guillaume and Adamcik, Jozef and Dietler, Giovanni},
     16919  title = {{Persistence length and scaling properties of single-stranded DNA adsorbed on modified graphite}},
     16920  journal = {{Journal of Chemical Physics}},
     16921  year = {2009},
     16922  volume = {{131}},
     16923  number = {{9}},
     16924  pages = {{095103}}
     16925}
     16926@article{Graff2006,
     16927  author = {Graff, Mason and Frazier, A. Bruno},
     16928  title = {{Resonance Light Scattering (RLS) Detection of Nanoparticle Separations in a Microelectrical Field-Flow Fractionation System}},
     16929  journal = {{IEEE Transactions on Nanotechnology}},
     16930  year = {2006},
     16931  volume = {{5}},
     16932  number = {{1}},
     16933  pages = {{8-13}}
     16934}
     16935@article{Kao1994,
     16936  author = {Kao, H.P. and Verkman, A.S.},
     16937  title = {{Tracking of single fluorescent particles in three dimensions: use of cylindrical optics to encode particle position}},
     16938  journal = {{Biophysical Journal}},
     16939  year = {1994},
     16940  volume = {{67}},
     16941  number = {{3}},
     16942  pages = {{1291-1300}}
     16943}
     16944@article{Jo2007,
     16945  author = {Jo, Kyubong and Dhingra, Dalia M. and Odijk, Theo and de Pablo, Juan J. and Graham, Michael D. and Runnheim, Rod and Forrest, Dan and Schwartz, David C.},
     16946  title = {{A single-molecule barcoding system using nanoslits for DNA analysis}},
     16947  journal = {{Proceedings of the National Academy of Sciences of the USA}},
     16948  year = {2007},
     16949  volume = {{104}},
     16950  number = {{8}},
     16951  pages = {{2673-2678}}
     16952}
     16953@article{Speidel2003,
     16954  author = {Speidel, Michael and Jonas, Alexandr and Florin, Ernst-Ludwig},
     16955  title = {{Three-dimensional tracking of fluorescent nanoparticles with subnanometer precision by use of off-focus imaging}},
     16956  journal = {{Optics Letters}},
     16957  year = {2003},
     16958  volume = {{28}},
     16959  number = {{2}},
     16960  pages = {{69-71}}
     16961}
     16962@article{Pounder2006,
     16963  author = {Pounder, June I. and Aldous, Wade K. and Woods, Gail L.},
     16964  title = {{Comparison of real-time polymerase chain reaction using the Smart Cycler and the Gen-Probe amplified Mycobacterium tuberculosis direct test for detection of M. tuberculosis complex in clinical specimens }},
     16965  journal = {{Diagnostic Microbiology and Infectious Disease}},
     16966  year = {2006},
     16967  volume = {{54}},
     16968  number = {{3}},
     16969  pages = {{217-222}}
     16970}
     16971@article{Harris1966,
     16972  author = {Harris, R.A. and Hearst, J.E.},
     16973  title = {{On Polymer Dynamics}},
     16974  journal = {{The Journal of Chemical Physics}},
     16975  year = {1966},
     16976  volume = {{44}},
     16977  number = {{7}},
     16978  pages = {{2595}}
     16979}
     16980@article{Willert1992,
     16981  author = {Willert, C. E. and Gharib, M.},
     16982  title = {{Three-dimensional particle imaging with a single camera}},
     16983  journal = {{Experiments in Fluids}},
     16984  year = {1992},
     16985  volume = {{12}},
     16986  pages = {{353-358}}
     16987}
     16988@article{Oberholzer1997,
     16989  author = {Oberholzer, Matthew R. and Wagner, Norman J. and Lenhoff, Abraham M.},
     16990  title = {{Grand canonical Brownian dynamics simulation of colloidal adsorption}},
     16991  journal = {{Journal of Chemical Physics}},
     16992  year = {1997},
     16993  volume = {{107}},
     16994  number = {{21}},
     16995  pages = {{9157-9167}}
     16996}
     16997@article{Wiggins2006,
     16998  author = {Wiggins, Paul A. and Nelson, Philip C.},
     16999  title = {{Generalized theory of semiflexible polymers}},
     17000  journal = {{Physical Review E}},
     17001  year = {2006},
     17002  volume = {{73}}
     17003}
     17004@article{Brenner1961,
     17005  author = {Brenner, Howard},
     17006  title = {{The slow motion of a sphere through a viscous fluid towards a plane surface}},
     17007  journal = {{Chemical Engineering Science}},
     17008  year = {1961},
     17009  volume = {{16}},
     17010  number = {{3-4}},
     17011  pages = {{242-251}}
     17012}
     17013@article{Bhattacharjee1987,
     17014  author = {Bhattacharjee, Somendra M. and Muthukumar, M.},
     17015  title = {{Statistical mechanics of solutions of semiflexible chains: A path integral formulation}},
     17016  journal = {{the Journal of Chemical Physics}},
     17017  year = {1987},
     17018  volume = {{86}},
     17019  number = {{1}},
     17020  pages = {{411-418}}
     17021}
     17022@article{Armani2007,
     17023  author = {Armani, Andrea M. and Kulkarni, Rajan P. and Fraser, Scott E. and Flagan, Richard C. and Vahala, Kerry J.},
     17024  title = {{Label-Free, Single-Molecule Detection with Optical Microcavities}},
     17025  journal = {{Sciencexpress}},
     17026  year = {2007}
     17027}
     17028@article{Hegner1999,
     17029  author = {Hegner, Martin and Smith, Steven B. and Bustamante, Carlos},
     17030  title = {{Polymerization and mechanical properties of single RecA-DNA filaments}},
     17031  journal = {{Proceedings of the National Academy of Sciences of the USA}},
     17032  year = {1999},
     17033  volume = {{96}},
     17034  number = {{18}},
     17035  pages = {{10109-10114}}
     17036}
     17037@article{Zhu2001,
     17038  author = {Zhu, Heng and Snyder, Michael},
     17039  title = {{Protein arrays and microarrays}},
     17040  journal = {{Current Opinion in Chemical Biology}},
     17041  year = {2001},
     17042  volume = {{5}},
     17043  number = {{1}},
     17044  pages = {{40-45}}
     17045}
     17046@article{Wiggins2006b,
     17047  author = {Wiggins, P. A. and van der Heijden, T. and Moreno-Herrero, F. and Spakowitz, A. and Philips, R. and Windom, J. and Dekker, C. and Nelson, P. C.},
     17048  title = {{High flexibility of DNA on short length scales probed by atomic force microscopy}},
     17049  journal = {{Nature Nanotechnology}},
     17050  year = {2006},
     17051  volume = {{1}},
     17052  pages = {{137-141}}
     17053}
     17054@article{Zhang2007,
     17055  author = {Zhang, Bo and Zerubia, Josiane and Olivo-Marin, Jean-Christophe},
     17056  title = {{Gaussian approximations of fluorescence microscope point-spread function models}},
     17057  journal = {{Applied Optics}},
     17058  year = {2007},
     17059  volume = {{46}},
     17060  number = {{10}},
     17061  pages = {{1819-1829}}
     17062}
     17063@article{Scott1979,
     17064  author = {Scott, David W.},
     17065  title = {{On optimal and data-based histograms}},
     17066  journal = {{Biometrika}},
     17067  year = {1979},
     17068  volume = {{66}},
     17069  number = {{3}},
     17070  pages = {{605-610}}
     17071}
     17072@article{Mlodzianoski2009,
     17073  author = {Mlodzianoski, Michael J. and Juette, Manuel F. and Beane, Glen L. and Bewersdorf, Joerg},
     17074  title = {{Experimental characterization of 3D localization techniques for particle-tracking and super-resolution microscopy}},
     17075  journal = {{Optics Express}},
     17076  year = {2009},
     17077  volume = {{17}},
     17078  number = {{10}},
     17079  pages = {{8264-8277}}
     17080}
     17081@article{Carre2003,
     17082  author = {Carr\\\'e, Alain and Lacarri\\\`ere, Val\\\'erie and Birch, William},
     17083  title = {{Molecular interactions between DNA and an aminated glass substrate}},
     17084  journal = {{Journal of Colloid and Interface Science}},
     17085  year = {2003},
     17086  volume = {{260}},
     17087  pages = {{49-55}}
     17088}
     17089@article{Sage2005,
     17090  author = {Sage, Daniel and Neumann, Franck R. and Hediger, Florence and Gasser, Susan M. and Unser, Michael},
     17091  title = {{Automatic Tracking of Individual Fluorescence Particles: Application to the Study of Chromosome Dynamics}},
     17092  journal = {{IEEE Transactions on Image Processing}},
     17093  year = {2005},
     17094  volume = {{14}},
     17095  number = {{9}},
     17096  pages = {{1372-1383}}
     17097}
     17098@article{Dohoney2001,
     17099  author = {Dohoney, Kathleen M. and Gelles, Jeff},
     17100  title = {{Chi-Sequence recognition and DNA translocation by single RecBCD helicase/nuclease molecules}},
     17101  journal = {{Nature}},
     17102  year = {2001},
     17103  volume = {{409}},
     17104  pages = {{370-374}}
     17105}
     17106@article{Saleh2009,
     17107  author = {Saleh, O.A. and McIntosh, D.B. and Pincus, P. and Ribeck, N.},
     17108  title = {{Nonlinear Low-Force Elasticity of Single-Stranded DNA Molecules}},
     17109  journal = {{Physical Review Letters}},
     17110  year = {2009},
     17111  volume = {{102}},
     17112  number = {{6}},
     17113  pages = {{068301}}
     17114}
     17115@article{Moerner2007,
     17116  author = {Moerner, W.E.},
     17117  title = {{New directions in single-molecule imaging and analysis}},
     17118  journal = {{Proceedings of the National Academy of Sciences of the USA}},
     17119  year = {2007},
     17120  volume = {{104}},
     17121  number = {{31}},
     17122  pages = {{12596-12602}}
     17123}
     17124@article{Spakowitz2005,
     17125  author = {Spakowitz, Andrew J. and Wang, Zhen-Gang},
     17126  title = {{End-to-end distance vector distribution with fixed end orientations for the wormlike chain model}},
     17127  journal = {{Physical Review E}},
     17128  year = {2005},
     17129  volume = {{72}}
     17130}
     17131@article{Spakowitz2004,
     17132  author = {Spakowitz, Andrew J. and Wang, Zhen-Gang},
     17133  title = {{Exact Results for a Semiflexible Polymer Chain in an Aligning Field}},
     17134  journal = {{Macromolecules}},
     17135  year = {2004},
     17136  volume = {{37}},
     17137  pages = {{5814-5823}}
     17138}
     17139@article{Spakowitz2006,
     17140  author = {Spakowitz, A. J.},
     17141  title = {{Wormlike chain statistics with twist and fixed ends}},
     17142  journal = {{Europhysics Letters (EPL)}},
     17143  year = {2006},
     17144  volume = {{73}},
     17145  number = {{5}},
     17146  pages = {{684-690}}
     17147}
     17148@article{Wieser2008,
     17149  author = {Wieser, Stefan and Axmann, Markus and Sch\\\"utz, Gerhard J.},
     17150  title = {{Versatile Analysis of Single-Molecule Tracking Data by Comprehensive Testing against Monte Carlo Simulations}},
     17151  journal = {{Biophysical Journal}},
     17152  year = {2008},
     17153  volume = {{95}},
     17154  number = {{12}},
     17155  pages = {{5988-6001}}
     17156}
     17157@phdthesis{Sarkar2002,
     17158  author = {Sarkar, Abhijit},
     17159  title = {{Theoretical micromechanics of DNA and DNA-protein complexes}},
     17160  year = {2002},
     17161  school = {{University of Illinois at Chicago}}
     17162}
     17163@article{Ha1995,
     17164  author = {Ha, B.-Y. and Thirumalai, D.},
     17165  title = {{A mean-field model for semiflexible chains}},
     17166  journal = {{Journal of Chemical Physics}},
     17167  year = {1995},
     17168  volume = {{103}},
     17169  number = {{21}},
     17170  pages = {{9408-9412}}
     17171}
     17172@misc{Beausang2006,
     17173  author = {Beausang, John F. and Zurla, Chiara and Sullivan, Luke and Finzi, Laura and Nelson, Philip C.},
     17174  title = {{Elementary simulation of tethered Brownian motion}},
     17175  year = {2006},
     17176  month = {October 1, 2006}
     17177}
     17178@article{Beausang2007,
     17179  author = {Beausang, John F. and Zurla, Chiara and Finzi, Laura and Sullivan, Luke and Nelson, Philip C.},
     17180  title = {{Elementary simulation of tethered Brownian motion}},
     17181  journal = {{American Journal of Physics}},
     17182  year = {2007},
     17183  volume = {{75}},
     17184  number = {{6}},
     17185  pages = {{520-523}}
     17186}
     17187@phdthesis{Guasto2008,
     17188  author = {Guasto, Jeffrey S.},
     17189  title = {{Micro- and Nano-scale Colloidal Dynamics Near Surfaces}},
     17190  year = {2008},
     17191  school = {{Brown University}}
     17192}
     17193@misc{Nelson2001,
     17194  author = {Nelson, Edward},
     17195  title = {{Dynamical Theories of Brownian Motion}},
     17196  year = {2001},
     17197  volume = {Second edition},
     17198  publisher = {{Princeton University Press}}
     17199}
     17200@article{Shivashankar1998,
     17201  author = {Shivashankar, G.V. and Stolovitzky, G. and Libchaber, A.},
     17202  title = {{Backscattering from a tethered bead as a probe of DNA flexibility}},
     17203  journal = {{Applied Physics Letters}},
     17204  year = {1998},
     17205  volume = {{73}},
     17206  number = {{3}},
     17207  pages = {{291-293}}
     17208}
     17209@phdthesis{Niu2004,
     17210  author = {Niu, Sanjun},
     17211  title = {{A Label-free, Fluorescence Based Assay for Microarray}},
     17212  year = {2004},
     17213  school = {{Virginia Polytechnic Institute and State University}}
     17214}
     17215@article{Hiraoka1987,
     17216  author = {Hiraoka, Yasushi and Sedat, John W. and Agard, David A.},
     17217  title = {{The Use of a Charge-Coupled Device for Quantitative Optical Microscopy of Biological Structures}},
     17218  journal = {{Science}},
     17219  year = {1987},
     17220  volume = {{238}},
     17221  pages = {{36-41}}
     17222}
     17223@article{Yamakawa1976,
     17224  author = {Yamakawa, Hiromi and Fujii, Motoharu and Shimada, Jiro},
     17225  title = {{Statistical mechanics of helical wormlike chains. II. Operational method and moments}},
     17226  journal = {{The Journal of Chemical Physics}},
     17227  year = {1976},
     17228  volume = {{65}},
     17229  number = {{6}},
     17230  pages = {{2371-2376}}
     17231}
     17232@article{Nelson2007,
     17233  author = {Nelson, Philip C.},
     17234  title = {{Colloidal particle motion as a diagnostic of DNA conformational transitions}},
     17235  journal = {{Current Opinion in Colloid & Interface Science}},
     17236  year = {2007}
     17237}
     17238@article{Allemand2003,
     17239  author = {Allemand, Jean-Francois and Bensimon, David and Croquette, Vincent},
     17240  title = {{Stretching DNA and RNA to probe their interactions with proteins}},
     17241  journal = {{Current Opinion in Structural Biology}},
     17242  year = {2003},
     17243  volume = {{13}},
     17244  pages = {{266-274}}
     17245}
     17246@article{Liu2007,
     17247  author = {Liu, Gang Logan and Long, Yi-Tao and Choi, Yeonho and Kang, Taewook and Lee, Luke P.},
     17248  title = {{Quantized plasmon quenching dips nanospectroscopy via plasmon resonance energy transfer}},
     17249  journal = {{Nature Methods}},
     17250  year = {2007},
     17251  volume = {{4}},
     17252  number = {{12}},
     17253  pages = {{1015-1017}}
     17254}
     17255@article{Prieve1990,
     17256  author = {Prieve, Dennis C. and Frej, Nasser A.},
     17257  title = {{Total Internal Reflection Microscopy: a Tool for Measuring Colloidal Forces}},
     17258  journal = {{Langmuir}},
     17259  year = {1990},
     17260  volume = {{6}},
     17261  number = {{2}},
     17262  pages = {{396-403}}
     17263}
     17264@article{Strick1996,
     17265  author = {Strick, T.R. and Allemand, J.-F. and Bensimon, D. and Bensimon, A. and Croquette, V.},
     17266  title = {{The Elasticity of a Single Supercoiled DNA Molecule}},
     17267  journal = {{Science}},
     17268  year = {1996},
     17269  volume = {{271}},
     17270  number = {{5257}},
     17271  pages = {{1835-1837}}
     17272}
     17273@article{Prieve1993,
     17274  author = {Prieve, Dennis C. and Walz, John Y.},
     17275  title = {{Scattering of an evanescent surface wave by a microscopic dielectric sphere}},
     17276  journal = {{Applied Optics}},
     17277  year = {1993},
     17278  volume = {{32}},
     17279  number = {{9}}
     17280}
     17281@article{Montanari2001,
     17282  author = {Montanari, Andrea and M\\\'ezard, Marc},
     17283  title = {{Hairpin Formation and Elongation of Biomolecules}},
     17284  journal = {{Physical Review Letters}},
     17285  year = {2001},
     17286  volume = {{86}},
     17287  number = {{10}},
     17288  pages = {{2178-2181}}
     17289}
     17290@article{Storm2003b,
     17291  author = {Storm, C. and Nelson, P. C.},
     17292  title = {{Theory of high-force DNA stretching and overstretching}},
     17293  journal = {{Physical Review E}},
     17294  year = {2003},
     17295  volume = {{67}},
     17296  number = {{5}},
     17297  pages = {{051906}}
     17298}
     17299@article{Bouchiat1999,
     17300  author = {Bouchiat, C. and Wang, M. D. and Allemand, J.-F. and Strick, T. and Block, S. M. and Croquette, V.},
     17301  title = {{Estimating the Persistence Length of a Worm-Like Chain Molecule from Force-Extension Measurements}},
     17302  journal = {{Biophysical Journal}},
     17303  year = {1999},
     17304  volume = {{76}},
     17305  pages = {{409-413}}
     17306}
     17307@article{Cady2007,
     17308  author = {Cady, Nathaniel C. and Strickland, Aaron D. and Batt, Carl A.},
     17309  title = {{Optimized linkage and quenching strategies for quantum dot molecular beacons}},
     17310  journal = {{Molecular and Cellular Probes}},
     17311  year = {2007},
     17312  volume = {{21}},
     17313  pages = {{116-124}}
     17314}
     17315@article{Fraden1993,
     17316  author = {Fraden, Seth and Maret, Georg},
     17317  title = {{Angular correlations and the isotropic-nematic phase transition in suspensions of tobacco mosaic virus}},
     17318  journal = {{Physical Review E}},
     17319  year = {1993},
     17320  volume = {{48}},
     17321  number = {{4}},
     17322  pages = {{2816-2838}}
     17323}
     17324@article{Bustamante1994,
     17325  author = {Bustamante, C. and Marko, J.F. and Siggia, E.D. and Smith, S.},
     17326  title = {{Entropic Elasticity of lambda-Phage DNA}},
     17327  journal = {{Science}},
     17328  year = {1994},
     17329  volume = {{265}},
     17330  number = {{5178}},
     17331  pages = {{1599-1601}}
     17332}
     17333@article{Rouse1953,
     17334  author = {Rouse, Prince E.},
     17335  title = {{A Theory of the Linear Viscoelastic Properties of Dilute Solutions of Coiling Polymers}},
     17336  journal = {{The Journal of Chemical Physics}},
     17337  year = {1953},
     17338  volume = {{21}},
     17339  number = {{7}},
     17340  pages = {{1272-1280}}
     17341}
     17342@article{Vanzi2003,
     17343  author = {Vanzi, Francesco and Vladimirov, Serguei and Knudsen, Charlotte R. and Goldman, Yale E. and Cooperman, Barry S.},
     17344  title = {{Protein synthesis by single ribosomes}},
     17345  journal = {{RNA}},
     17346  year = {2003},
     17347  volume = {{9}},
     17348  number = {{10}},
     17349  pages = {{1174-1179}}
     17350}
     17351@article{Lambert2006,
     17352  author = {Lambert, Meredith Newby and V\\\"ocker, Eva and Blumberg, Seth and Redemann, Stefanie and Gajraj, Arivalagan and Meiners, Jens-Christian and Walter, Nils. G.},
     17353  title = {{Mg2+-Induced Compaction of Single RNA Molecules Monitored by Tethered Particle Microscopy}},
     17354  journal = {{Biophysical Journal}},
     17355  year = {2006},
     17356  volume = {{90}},
     17357  pages = {{3672-3685}}
     17358}
     17359@article{Kessler2004,
     17360  author = {Kessler, David A. and Rabin, Yitzhak},
     17361  title = {{Distribution functions for filaments under tension}},
     17362  journal = {{Journal of Chemical Physics}},
     17363  year = {2004},
     17364  volume = {{121}},
     17365  number = {{2}},
     17366  pages = {{1155-1164}}
     17367}
     17368@article{Edwards1970,
     17369  author = {Edwards, S.F.},
     17370  title = {{Theory of the Single Chain}},
     17371  journal = {{Discussions of the Faraday Society}},
     17372  year = {1970},
     17373  volume = {{49}},
     17374  pages = {{43}}
     17375}
     17376@article{Bouzigues2008,
     17377  author = {Bouzigues, C. I. and Tabeling, P. and Bocquet, L.},
     17378  title = {{Nanofluidics in the Debye Layer at Hydrophilic and Hydrophobic Surfaces}},
     17379  journal = {{Physical Review Letters}},
     17380  year = {2008},
     17381  volume = {{101}},
     17382  number = {{11}},
     17383  pages = {{114503}}
     17384}
     17385@misc{Odijk2008,
     17386  author = {Odijk, Theo},
     17387  title = {{Private communication}},
     17388  year = {2008},
     17389  month = {05 September 2008}
     17390}
     17391@article{Kirkpatrick2008,
     17392  author = {Kirkpatrick, S.J. and Duncan, D.D.},
     17393  title = {{Performance of a gradient-based shift estimator in a spatially sparse data environment: tracking the sub-pixel motion of fluorescent particles}},
     17394  journal = {{Journal of Microscopy}},
     17395  year = {2008},
     17396  volume = {{212}},
     17397  number = {{1}},
     17398  pages = {{64-72}}
     17399}
     17400@article{Visnapuu2009,
     17401  author = {Visnapuu, Mari-Liis and Greene, Eric C.},
     17402  title = {{Single-molecule imaging of DNA curtains reveals intrinsic energy landscapes for nucleosome deposition}},
     17403  journal = {{Nature Structural & Molecular Biology}},
     17404  year = {2009},
     17405  volume = {{16}},
     17406  number = {{10}},
     17407  pages = {{1056-1062}}
     17408}
     17409@book{Conover1980,
     17410  author = {Conover, W.J.},
     17411  title = {{Practical Nonparametric Statistics}},
     17412  year = {1980},
     17413  publisher = {{Wiley}},
     17414  series = {{Wiley series in probability and mathematical statistics}},
     17415  address = {{New York}},
     17416  edition = {{Second edition}}
     17417}
     17418@article{Snyder1992,
     17419  author = {Snyder, Donald L. and Schulz, Timothy H. and O'Sullivan, Joseph A.},
     17420  title = {{Deblurring Subject to Nonnegativity Constraints}},
     17421  journal = {{IEEE Transactions on Signal Processing}},
     17422  year = {1992},
     17423  volume = {{40}},
     17424  number = {{5}},
     17425  pages = {{1143-1150}}
     17426}
     17427@article{DiMarzio1965b,
     17428  author = {DiMarzio, Edmund A. and McCrackin, Frank L.},
     17429  title = {{One-Dimensional Model of Polymer Adsorption}},
     17430  journal = {{The Journal of Chemical Physics}},
     17431  year = {1965},
     17432  volume = {{43}},
     17433  number = {{2}}
     17434}
     17435@article{DiMarzio1965a,
     17436  author = {DiMarzio, Edmund A.},
     17437  title = {{Proper Accounting of Conformations of a Polymer Near a Surface}},
     17438  journal = {{The Journal of Chemical Physics}},
     17439  year = {1965},
     17440  volume = {{42}},
     17441  number = {{6}},
     17442  pages = {{2101-2106}}
     17443}
     17444@article{Netopilik1990,
     17445  author = {Netopil\\\'{\\\i}k, M.},
     17446  title = {{Orientation-dependent rotational diffusion coefficient of rod-like macromolecules in semi-dilute solution}},
     17447  journal = {{Rheologica Acta}},
     17448  year = {1990},
     17449  volume = {{29}},
     17450  pages = {{172-173}}
     17451}
     17452@article{Hamaker1937,
     17453  author = {Hamaker, H.C.},
     17454  title = {{The London-Van Der Waals Attraction Between Spherical Particles}},
     17455  journal = {{Physica }},
     17456  year = {1937},
     17457  volume = {{4}},
     17458  number = {{10}},
     17459  pages = {{1058-1072}}
     17460}
     17461@article{Cheezum2001,
     17462  author = {Cheezum, Michael K. and Walker, William F. and Guilford, William H.},
     17463  title = {{Quantitative Comparison of Algorithms for Tracking Single Fluorescent Particles}},
     17464  journal = {{Biophysical Journal}},
     17465  year = {2001},
     17466  volume = {{81}},
     17467  number = {{4}},
     17468  pages = {{2378-2388}}
     17469}
     17470@article{Ritchie2005,
     17471  author = {Ritchie, Ken and Sha, Xiao-Yuan and Kondo, Junko and Iwasawa, Kokoro and Fujiwara, Takahiro and Kusumi, Akihiro},
     17472  title = {{Detection of Non-Brownian Diffusion in the Cell Membrane in Single Molecule Tracking}},
     17473  journal = {{Biophysical Journal}},
     17474  year = {2005},
     17475  volume = {{88}},
     17476  number = {{3}},
     17477  pages = {{2266-2277}}
     17478}
     17479@incollection{Han2009,
     17480  author = {Han, Lin and Lui, Bertrand and Blumberg, Seth and Beausang, John F. and Nelson, Philip C. and Philips, Rob},
     17481  title = {{Calibration of Tethered Particle Motion Experiments}},
     17482  year = {2009},
     17483  volume = {150},
     17484  editor = {Benham, C.J. and Harvey, S. and Olson, W.K. and Sumners, D.W. and Swigon, D.},
     17485  publisher = {{Springer}},
     17486  series = {{The IMA Volumes in Mathematics and its Applications}},
     17487  booktitle = {{Mathematics of DNA Structure, Funcion and Interactions}}
     17488}
     17489@article{Towles2009,
     17490  author = {Towles, Kevin B. and Beausang, John F. and Garcia, H.G. and Philips, Rob and Nelson, Philip C.},
     17491  title = {{First-principles calculation of DNA looping in tethered particle experiments}},
     17492  journal = {{Physical Biology}},
     17493  year = {2009},
     17494  volume = {{6}},
     17495  pages = {{025001}}
     17496}
     17497@article{Pralle1999,
     17498  author = {Pralle, A. and Prummer, M. and Florin, E.-L and Stelzer, E.H.K. and H\\\"orber, J.K.H.},
     17499  title = {{Three-Dimensional High-resolution Particle Tracking for Optical Tweezers by Forward Scattered Light}},
     17500  journal = {{Microscopy Research and Technique}},
     17501  year = {1999},
     17502  volume = {{44}},
     17503  number = {{5}},
     17504  pages = {{378-386}}
     17505}
     17506@article{Wrobel2003,
     17507  author = {Wrobel, Gunnar and Schlingemann, Joerg and Hummerich, Lars and Kramer, Heidi and Lichter, Peter and Hahn, Meinhard},
     17508  title = {{Optimization of high-density cDNA-microarray protocols by 'design of experiments'}},
     17509  journal = {{Nucleic Acids Research}},
     17510  year = {2003},
     17511  volume = {{131}},
     17512  number = {{12}}
     17513}
     17514@article{Gibson1989,
     17515  author = {Gibson, Sarah Frisken and Lanni, Frederick},
     17516  title = {{Diffraction by a Circular Aperture as a Model for Three-Dimensional Microscopy}},
     17517  journal = {{Journal of the Optical Society of America A}},
     17518  year = {1989},
     17519  volume = {{6}},
     17520  number = {{9}},
     17521  pages = {{1357-1367}}
     17522}
     17523@article{Destainville2006,
     17524  author = {Destainville, Nicolas and Salom\\\'e, Laurence},
     17525  title = {{Quantification and Correction of Systematic Erros Due to Detector Time-Averaging in Single-Molecule Tracking Experiments}},
     17526  journal = {{Biophysical Journal}},
     17527  year = {2006},
     17528  volume = {{90}},
     17529  number = {{2}},
     17530  pages = {{L17-L19}}
     17531}
     17532@article{Sader1997,
     17533  author = {Sader, John Elie},
     17534  title = {{Accurate Analytic Formulae for the Far Field Effective Potential and Surface Charge Density of a Uniformly Charged Sphere}},
     17535  journal = {{Journal of Colloid and Interface Science}},
     17536  year = {1997},
     17537  volume = {{188}},
     17538  number = {{2}},
     17539  pages = {{508-510}}
     17540}
     17541@article{Durnin1987,
     17542  author = {Durnin, J. and Miceli, J.J., Jr. and Eberly, J.H.},
     17543  title = {{Diffraction-Free Beams}},
     17544  journal = {{Physical Review Letters}},
     17545  year = {1987},
     17546  volume = {{58}},
     17547  number = {{15}},
     17548  pages = {{1499-1501}}
     17549}
     17550@article{Moroz1998,
     17551  author = {Moroz, J. David and Nelson, Philip},
     17552  title = {{Entropic Elasticity of Twist-Storing Polymers}},
     17553  journal = {{Macromolecules}},
     17554  year = {1998},
     17555  volume = {{31}},
     17556  pages = {{6333-6347}}
     17557}
     17558@article{Peters1998,
     17559  author = {Peters, Inge M. and de Grooth, Bart G. and Schins, Juleon M. and Figdor, Carl G. and Greve, Jan},
     17560  title = {{Three dimensional single-particle tracking with nanometer resolution}},
     17561  journal = {{Review of Scientific Instruments}},
     17562  year = {1998},
     17563  volume = {{69}},
     17564  number = {{7}},
     17565  pages = {{2762-2766}}
     17566}
     17567@article{Kessler1991,
     17568  author = {Kessler, Christoph},
     17569  title = {{The digoxigenin:anti-digoxigening (DIG) technology - a survey on the concept and realization of a novel bioanalytical indicator system}},
     17570  journal = {{Molecular and Cellular Probes}},
     17571  year = {1991},
     17572  volume = {{5}},
     17573  pages = {{161-205}}
     17574}
     17575@article{Hyeon2006a,
     17576  author = {Hyeon, Changbong and Thirumalai, D.},
     17577  title = {{Kinetics of interior loop formation in semiflexible chains}},
     17578  journal = {{The Journal of Chemical Physics}},
     17579  year = {2006},
     17580  volume = {{124}},
     17581  number = {{10}},
     17582  pages = {{104905}}
     17583}
     17584@article{Moroz1997,
     17585  author = {Moroz, J. David and Nelson, Philip},
     17586  title = {{Torsional directed walks, entropic elasticity, and DNA twist stiffness}},
     17587  journal = {{Proceedings of the National Academy of Sciences of the USA}},
     17588  year = {1997},
     17589  volume = {{94}},
     17590  number = {{26}},
     17591  pages = {{14418-14422}}
     17592}
     17593@article{Massart2005,
     17594  author = {Massart, D.L. and Smeyers-Verbeke, J. and Capron, X. and Schlesier, Karin},
     17595  title = {{Visual Presentation of Data by Means of Box Plots}},
     17596  journal = {{LC-GC Europe}},
     17597  year = {2005},
     17598  volume = {{18}},
     17599  number = {{4}},
     17600  pages = {{215-218}}
     17601}
     17602@article{Hynes2001,
     17603  author = {Hynes, N. E. and Horsch, K. and Olayioye, M. A. and Badache, A.},
     17604  title = {The ErbB receptor tyrosine family as signal integrators},
     17605  journal = {Endocr Relat Cancer},
     17606  year = {2001},
     17607  volume = {8},
     17608  number = {3},
     17609  pages = {151-9}
     17610}
     17611@article{Michalet2001,
     17612  author = {Michalet, X. and Pinaud, F. and Lacoste, T. D. and Dahan, M. and Bruchez, M. P. and Alivisatos, A. P. and Weiss, S.},
     17613  title = {Properties of fluorescent semiconductor nanocrystals and their application to biological labeling},
     17614  journal = {Single Molecules},
     17615  year = {2001},
     17616  volume = {2},
     17617  number = {4},
     17618  pages = {261-276}
     17619}
     17620@article{Kuno2001,
     17621  author = {Kuno, M. and Fromm, D. P. and Hamann, H. F. and Gallagher, A. and Nesbitt, D. J.},
     17622  title = {"On"/"off" fluorescence intermittency of single semiconductor quantum dots},
     17623  journal = {Journal of Chemical Physics},
     17624  year = {2001},
     17625  volume = {115},
     17626  number = {2},
     17627  pages = {1028-1040}
     17628}
     17629@article{Martinez2003,
     17630  author = {Martinez, M. J. and Aragon, A. D. and Rodriguez, A. L. and Weber, J. M. and Timlin, J. A. and Sinclair, M. B. and Haaland, D. M. and Werner-Washburne, M.},
     17631  title = {Identification and removal of contaminating fluorescence from commercial and in-house printed DNA microarrays},
     17632  journal = {Nucleic Acids Research},
     17633  year = {2003},
     17634  volume = {31},
     17635  number = {4},
     17636  pages = {e18}
     17637}
     17638@article{Stauffer1997,
     17639  author = {Stauffer, T. P. and Meyer, T.},
     17640  title = {Compartmentalized IgE receptor-mediated signal transduction in living cells},
     17641  journal = {J Cell Biol},
     17642  year = {1997},
     17643  volume = {139},
     17644  number = {6},
     17645  pages = {1447-54}
     17646}
     17647@article{Hebert2005,
     17648  author = {Hebert, B. and Costantino, S. and Wiseman, P. W.},
     17649  title = {Spatiotemporal image correlation Spectroscopy (STICS) theory, verification, and application to protein velocity mapping in living CHO cells},
     17650  journal = {Biophysical Journal},
     17651  year = {2005},
     17652  volume = {88},
     17653  number = {5},
     17654  pages = {3601-3614}
     17655}
     17656@article{Pyenta2003,
     17657  author = {Pyenta, P. and Schwille, P. and Webb, W. and Holowka, D. and Baird, B.},
     17658  title = {Lateral diffusion of membrane lipid-anchored probes before and after aggregation of cell surface IgE-receptors},
     17659  journal = {J. Phys. Chem. A},
     17660  year = {2003},
     17661  volume = {107},
     17662  pages = {8310-8318}
     17663}
     17664@misc{CUDA,
     17665  author = {NVIDIA},
     17666  title = {Compute Unified Device Architecture (CUDA)},
     17667  year = {2007},
     17668  note = {{http://www.nvidia.com}}
     17669}
     17670@article{Petersen1993,
     17671  author = {Petersen, N. and Hoddelius, P.L. and Wiseman, P. and Seger, O. and Magnusson, K.},
     17672  title = {Quantitation of membrane receptor distributions by image correlation spectroscopy: concept and application},
     17673  journal = {Biophys. J.},
     17674  year = {1993},
     17675  volume = {65},
     17676  pages = {1135-1146}
     17677}
     17678@article{Hess2006,
     17679  author = {Hess, S. T. and Girirajan, T. P. K. and Mason, M. D.},
     17680  title = {Ultra-high resolution imaging by fluorescence photoactivation localization microscopy},
     17681  journal = {Biophysical Journal},
     17682  year = {2006},
     17683  volume = {91},
     17684  number = {11},
     17685  pages = {4258-4272}
     17686}
     17687@article{Kotula2004,
     17688  author = {Kotula, P. G. and Keenan, M. R. and Michael, J. R. },
     17689  title = {Automated analysis of SEM X-Ray spectral images: a powerful new microanalysis tool},
     17690  journal = {Microscopy and Microanalysis },
     17691  year = {2004},
     17692  volume = {9},
     17693  pages = {1-17}
     17694}
     17695@article{Yarden2001,
     17696  author = {Yarden, Y. and Sliwkowski, M. X.},
     17697  title = {Untangling the ErbB signalling network},
     17698  journal = {Nat Rev Mol Cell Biol},
     17699  year = {2001},
     17700  volume = {2},
     17701  number = {2},
     17702  pages = {127-37}
     17703}
     17704@article{MinGW,
     17705  author = {MinGW},
     17706  title = {Minimalist GNU for Windows},
     17707  year = {2008},
     17708  url = {http://www.mingw.org/}
     17709}
     17710@article{Shroff2008,
     17711  author = {Shroff, H. and Galbraith, C. G. and Galbraith, J. A. and Betzig, E.},
     17712  title = {Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics},
     17713  journal = {Nature Methods},
     17714  year = {2008},
     17715  volume = {5},
     17716  number = {5},
     17717  pages = {417-423}
     17718}
     17719@book{Jain1988,
     17720  author = {Jain, A. and Dubes, R.},
     17721  title = {Algorithms for Clustering Data},
     17722  year = {1988},
     17723  publisher = {Prentice Hall}
     17724}
     17725@article{Grecco2004,
     17726  author = {Grecco, H. E. and Lidke, K. A. and Heintzmann, R. and Lidke, D. S. and Spagnuolo, C. and Martinez, O. E. and Jares-Erijman, E. A. and Jovin, T. M.},
     17727  title = {Ensemble and single particle photophysical proper-ties (Two-Photon excitation, anisotropy, FRET, lifetime, spectral conversion) of commercial quantum dots in solution and in live cells},
     17728  journal = {Microscopy Research and Technique},
     17729  year = {2004},
     17730  volume = {65},
     17731  number = {4-5},
     17732  pages = {169-179}
     17733}
     17734@article{VanBenthem2002,
     17735  author = {Van Benthem, M. H. and Keenan, M. R. and Haaland, D. M. },
     17736  title = {Application of equality constraints on variables during alternating least squares procedures},
     17737  journal = {Journal of Chemometrics},
     17738  year = {2002},
     17739  volume = {16},
     17740  pages = {613-622}
     17741}
     17742@article{Manley2008,
     17743  author = {Manley, S. and Gillette, J. M. and Patterson, G. H. and Shroff, H. and Hess, H. F. and Betzig, E. and Lippincott-Schwartz, J.},
     17744  title = {High-density mapping of single-molecule trajectories with photoactivated localization microscopy},
     17745  journal = {Nature Methods},
     17746  year = {2008},
     17747  volume = {5},
     17748  number = {2},
     17749  pages = {155-157}
     17750}
     17751@article{Wilson2000,
     17752  author = {Wilson, B. S. and Pfeiffer, J. R. and Oliver, J. M.},
     17753  title = {Observing FcepsilonRI signaling from the inside of the mast cell membrane},
     17754  journal = {Journal of Cell Biology},
     17755  year = {2000},
     17756  volume = {149},
     17757  number = {5},
     17758  pages = {1131-1142}
     17759}
     17760@article{Wilson2004,
     17761  author = {Wilson, B. S. and Steinberg, S. L. and Liederman, K. and Pfeiffer, J. R. and Surviladze, Z. and Zhang, J. and Samelson, L. E. and Yang, L. H. and Kotula, P. G. and Oliver, J. M.},
     17762  title = {Markers for detergent-resistant lipid rafts occupy distinct and dynamic domains in native membranes},
     17763  journal = {Molecular Biology of the Cell},
     17764  year = {2004},
     17765  volume = {15},
     17766  number = {6},
     17767  pages = {2580-2592}
     17768}
     17769@article{Timlin2005,
     17770  author = {Timlin, J. A. and Haaland, D. M. and Sinclair, M. B. and Aragon, A. D. and Martinez, M. J. and Werner-Washburne, M.},
     17771  title = {Hyperspectral microarray scanning: impact on the accuracy and reliability of gene expression data},
     17772  journal = {BMC Genomics},
     17773  year = {2005},
     17774  volume = {6},
     17775  number = {1},
     17776  pages = {72}
     17777}
     17778@article{Forney1973,
     17779  author = {Forney, G. D.},
     17780  title = {Viterbi Algorithm},
     17781  journal = {Proceedings of the Ieee},
     17782  year = {1973},
     17783  volume = {61},
     17784  number = {3},
     17785  pages = {268-278}
     17786}
     17787@article{Szent-Gyorgyi2008,
     17788  author = {Szent-Gyorgyi, C. and Schmidt, B. F. and Creeger, Y. and Fisher, G. W. and Zakel, K. L. and Adler, S. and Fitzpatrick, J. A. J. and Woolford, C. A. and Yan, Q. and Vasilev, K. V. and Berget, P. B. and Bruchez, M. P. and Jarvik, J. W. and Waggoner, A.},
     17789  title = {Fluorogen-activating single-chain antibodies for imaging cell surface proteins (vol 26, pg 235, 2008)},
     17790  journal = {Nature Biotechnology},
     17791  year = {2008},
     17792  volume = {26},
     17793  number = {4},
     17794  pages = {470-470}
     17795}
     17796@article{Andrews2008,
     17797  author = {Andrews, N. L. and Lidke, K. A. and Pfeiffer, J. R. and Burns, A. R. and Wilson, B. S. and Oliver, J. M. and Lidke, D. S.},
     17798  title = {Actin restricts Fc epsilon RI diffusion and facilitates antigen-induced receptor immobilization},
     17799  journal = {Nature Cell Biology},
     17800  year = {2008},
     17801  volume = {10},
     17802  number = {8},
     17803  pages = {955-963}
     17804}
     17805@inproceedings{Lidke2007ieee,
     17806  author = {Lidke, K. A. and Heintzmann, R.},
     17807  title = {Localization fluorescence microscopy using quantum dot blinking},
     17808  year = {2007},
     17809  pages = {936-939},
     17810  address = {Metro Washington DC, USA. },
     17811  booktitle = {4th IEEE International Symposium on Biomedical Imaging}
     17812}
     17813@article{test,
     17814  author = {bla},
     17815  title = {die},
     17816  journal = {bla},
     17817  year = {2010}
     17818}
     17819@article{Bates2007,
     17820  author = {Bates, M. and Huang, B. and Dempsey, G. T. and Zhuang, X.},
     17821  title = {Multicolor super-resolution imaging with photo-switchable fluorescent probes},
     17822  journal = {Science},
     17823  year = {2007},
     17824  volume = {317},
     17825  number = {5845},
     17826  pages = {1749-53}
     17827}
     17828@book{Bos2007,
     17829  author = {A. van den Bos},
     17830  title = {Parameter Estimation for Scientists and Engineers},
     17831  year = {2007},
     17832  publisher = {Wiley \& Sons},
     17833  address = {New Jersey}
     17834}
     17835@article{Wolter2009,
     17836  author = {Wolter, S. and Schuttpelz, M. and Tescherepanow, M. and Linde, van de S. and Heilemann, M. and Sauer, M.},
     17837  title = {Real-time computation of subdiffraction-resolution fluorescence images},
     17838  journal = {Journal of Microscopy},
     17839  year = {2010},
     17840  volume = {237},
     17841  number = {1},
     17842  pages = {12-22}
     17843}
     17844@article{Bock2007,
     17845  author = {Bock, H. and Geisler, C. and Wurm, C. A. and Von Middendorff, C. and Jakobs, S. and Schonle, A. and Egner, A. and Hell, S. W. and Eggeling, C.},
     17846  title = {Two-color far-field fluorescence nanoscopy based on photoswitchable emitters},
     17847  journal = {Applied Physics B-Lasers and Optics},
     17848  year = {2007},
     17849  volume = {88},
     17850  number = {2},
     17851  pages = {161-165}
     17852}
     17853@article{Rust2006,
     17854  author = {Rust, M. J. and Bates, M. and Zhuang, X. W.},
     17855  title = {Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM)},
     17856  journal = {Nature Methods},
     17857  year = {2006},
     17858  volume = {3},
     17859  number = {10},
     17860  pages = {793-795}
     17861}
     17862@article{Enderlein2006,
     17863  author = {Enderlein, J. and Toprak, E. and Selvin, P.R.},
     17864  title = {Polariztion effect on position accuracy of fluorophore localization},
     17865  journal = {Optics Express},
     17866  year = {2006},
     17867  volume = {14},
     17868  number = {18},
     17869  pages = {8112-8120}
     17870}
     17871@article{Enderlein2000,
     17872  author = {Enderlein, J.},
     17873  title = {Theoretical Study of detection of a dipole emitter through an objective with high numerical aperture},
     17874  journal = {Optics Letters},
     17875  year = {2000},
     17876  volume = {25},
     17877  number = {9},
     17878  pages = {634-636}
     17879}
     17880@article{Dahan2003,
     17881  author = {Dahan, M. and Levi, S. and Luccardini, C. and Rostaing, P. and Riveau, B. and Triller, A.},
     17882  title = {Diffusion dynamics of glycine receptors revealed by single-quantum dot tracking},
     17883  journal = {Science},
     17884  year = {2003},
     17885  volume = {302},
     17886  number = {5644},
     17887  pages = {442-445}
     17888}
     17889@misc{OberEstimationtool,
     17890  author = {Ober, R.J. and Ward, E.S.},
     17891  title = {Estimation tool},
     17892  year = {2009},
     17893  note = {University of Texas, Southwestern {http://www4.utsouthwestern.edu/wardlab}}
     17894}
     17895@article{Jin2007,
     17896  author = {Jin, S. and Haggie, P. M. and Verkman, A. S.},
     17897  title = {Single-particle tracking of membrane protein diffusion in a potential: Simulation, detection, and application to confined diffusion of CFTR Cl- channels},
     17898  journal = {Biophysical Journal},
     17899  year = {2007},
     17900  volume = {93},
     17901  number = {3},
     17902  pages = {1079-1088}
     17903}
     17904@article{Jin2007b,
     17905  author = {Jin, S. and Verkman, A. S.},
     17906  title = {Single particle tracking of complex diffusion in membranes: Simulation and detection of barrier, raft, and interaction phenomena},
     17907  journal = {Journal of Physical Chemistry B},
     17908  year = {2007},
     17909  volume = {111},
     17910  number = {14},
     17911  pages = {3625-3632}
     17912}
     17913@article{Rasnik2006,
     17914  author = {Rasnik, I. and McKinney, S. A. and Ha, T.},
     17915  title = {Nonblinking and longlasting single-molecule fluorescence imaging},
     17916  journal = {Nature Methods},
     17917  year = {2006},
     17918  volume = {3},
     17919  number = {11},
     17920  pages = {891-893}
     17921}
     17922@article{Hell1992,
     17923  author = {Hell, S. and Stelzer, E. H. K.},
     17924  title = {Fundamental Improvement of Resolution with a 4Pi-Confocal Fluorescence Microscope Using 2-Photon Excitation},
     17925  journal = {Optics Communications},
     17926  year = {1992},
     17927  volume = {93},
     17928  number = {5-6},
     17929  pages = {277-282}
     17930}
     17931@article{LidkeDS2007,
     17932  author = {Lidke, D. S. and Andrews, N. L. and Pfeiffer, J. R. and Jones, H. D. T. and Sinclair, M. B. and Haaland, D. M and Burns, A. R. and Wilson, B. S. and M., Oliver. J. and Lidke, K. A.},
     17933  title = {Exploring membrane protein dynamics by multicolor single quantum dot imaging using wide field, TIRF, and hyperspectral microscopy},
     17934  journal = {Proc. of SPIE},
     17935  year = {2007},
     17936  volume = {6448},
     17937  pages = {6448Y1-8}
     17938}
     17939@article{Warren1997,
     17940  author = {Warren, D. W. and Hackwell, J. A. and Gutierrez, D. J.},
     17941  title = {Compact prism spectrographs based on aplanatic principles},
     17942  journal = {Optical Engineering},
     17943  year = {1997},
     17944  volume = {36},
     17945  number = {4},
     17946  pages = {1174-1182}
     17947}
     17948@article{Schlessinger2002,
     17949  author = {Schlessinger, J.},
     17950  title = {Ligand-induced, receptor-mediated dimerization and activation of EGF receptor},
     17951  journal = {Cell},
     17952  year = {2002},
     17953  volume = {110},
     17954  number = {6},
     17955  pages = {669-72}
     17956}
Note: See TracChangeset for help on using the changeset viewer.