Changeset 108
- Timestamp:
- 10/08/10 16:18:30 (15 years ago)
- File:
-
- 1 edited
-
qipapers.bib (modified) (2 diffs)
Legend:
- Unmodified
- Added
- Removed
-
qipapers.bib
r107 r108 12453 12453 year = {2010} 12454 12454 } 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}, 12456 12457 title = {Single Molecule Detection Of Tuberculosis Nucleic Acid Using Dark Field Tethered Particle Motion}, 12457 12458 year = {2010}, 12459 pages = {1269}, 12458 12460 month = {April 14-17}, 12459 12461 address = {Rotterdam, The Netherlands}, 12460 organization= {IEEE International Symposium on Biomedical Imaging}12462 booktitle = {IEEE International Symposium on Biomedical Imaging} 12461 12463 } 12462 12464 @article{Cordes2010, … … 15465 15467 @article{Meyer2008, 15466 15468 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 15510 in 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 15522 fluorescence 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.
