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pages = {4015-4029}, - journal = {Biophysical Journal}, - volume = {86}, + title = {{Information Bounsd and Optimal Analysis of Dynamic Single Molecule Measurements}}, + pages = {{4015-4029}}, + journal = {{Biophysical Journal}}, + volume = {{86}}, author = {Watkins, Lucas P. and Yang, Haw} } @@ -16099,9 +16098,9 @@ @article{Blumberg2005, year = {2005}, - title = {Three-Dimensional Characterization of Tethered Microspheres by Total Internal Reflection Fluorescence Microscopy}, - pages = {1272-1281}, - journal = {Biophysical Journal}, - volume = {89}, - author = {Blumberg, S. and Gajraj, A. and Pennington, M.W.} + title = {{Three-Dimensional Characterization of Tethered Microspheres by Total Internal Reflection Fluorescence Microscopy}}, + pages = {{1272-1281}}, + journal = {{Biophysical Journal}}, + volume = {{89}}, + author = {Blumberg, Seth and Gajraj, Arivalagan and Pennington, Matthew W.} } @misc{Neumann2001, @@ -16114,19 +16113,19 @@ } @article{Ommering2010, - number = {15}, + number = {{15}}, year = {2010}, - title = {Mobility and height detection of particle labels in an optical evanescent wave biosensor with single-label resolution}, - pages = {155501}, - journal = {Journal of Physics D: Applied Physics}, - volume = {43}, - author = {van Ommering, Kim and Somers, P.A. and Koets, Marjo and Schleipen, J.J.H.B. and van Ijzendoorn, L.J. and Prins, M.W.J.} + title = {{Mobility and height detection of particle labels in an optical evanescent wave biosensor with single-label resolution}}, + pages = {{155501}}, + journal = {{Journal of Physics D: Applied Physics}}, + volume = {{43}}, + author = {van Ommering, Kim and Somers, Philip A. and Koets, Marjo and Schleipen, Jean J.H.B. and van Ijzendoorn, Leo J. and Prins, Menno W.J.} } @article{Heaton2001, - number = {7}, + number = {{7}}, year = {2001}, - title = {Electrostatic surface plasmon resonance: Direct electric field-induced hybridization and denaturation in monolayer nucleic acid films and label-free discrimination of base mismatches}, - pages = {3701-3704}, - journal = {Proceedings of the National Academy of Sciences of the USA}, - volume = {98}, + title = {{Electrostatic surface plasmon resonance: Direct electric field-induced hybridization and denaturation in monolayer nucleic acid films and label-free discrimination of base mismatches}}, + pages = {{3701-3704}}, + journal = {{Proceedings of the National Academy of Sciences of the USA}}, + volume = {{98}}, author = {Heaton, Richard J. and Peterson, Alexander W. and Georgiadis, Rosina M.} } @@ -16245,11 +16244,11 @@ } @article{Zimm1956, - number = {2}, + number = {{2}}, year = {1956}, - title = {Dynamics of Polymer Molecules in Dilute Solution: Viscoelasticity, Flow Birefringence and Dielectric Loss}, - pages = {269-278}, - journal = {The Journal of Chemical Physics}, - volume = {24}, - author = {Zimm, B.H.} + title = {{Dynamics of Polymer Molecules in Dilute Solution: Viscoelasticity, Flow Birefringence and Dielectric Loss}}, + pages = {{269-278}}, + journal = {{The Journal of Chemical Physics}}, + volume = {{24}}, + author = {Zimm, Bruno H.} } @article{Sadr2007, @@ -16259,13 +16258,13 @@ journal = {{Journal of Fluid Mechanics}}, volume = {{577}}, - author = {Sadr, Reza and Hohenegger, Christel and Li, Haifeng and Mucha, P.J. and Yoda, Minami} + author = {Sadr, Reza and Hohenegger, Christel and Li, Haifeng and Mucha, Peter J. and Yoda, Minami} } @article{Qian2000b, - number = {1}, + number = {{1}}, year = {2000}, - title = {Single-Particle Tracking: Brownian Dynamics of Viscoelastic Materials}, - pages = {137-143}, - journal = {Biophysical Journal}, - volume = {79}, + title = {{Single-Particle Tracking: Brownian Dynamics of Viscoelastic Materials}}, + pages = {{137-143}}, + journal = {{Biophysical Journal}}, + volume = {{79}}, author = {Qian, Hong} } @@ -16288,10 +16287,10 @@ } @article{Qian2000a, - number = {4}, + number = {{4}}, year = {2000}, - title = {A mathematical analysis for the Brownian dynamics of a {DNA} tether}, - pages = {331-340}, - journal = {Journal of Mathematical Biology}, - volume = {41}, + title = {{A mathematical analysis for the Brownian dynamics of a DNA tether}}, + pages = {{331-340}}, + journal = {{Journal of Mathematical Biology}}, + volume = {{41}}, author = {Qian, Hong} } @@ -16384,33 +16383,33 @@ } @article{Wong2006, - 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title = {{DNA} Persistencde Length Revisited}, - pages = {261-275}, - journal = {Biopolymers}, - volume = {61}, - author = {Lu, Y. and Weers, B. and Stellwagen, N.C.} + title = {{DNA Persistencde Length Revisited}}, + pages = {{261-275}}, + journal = {{Biopolymers}}, + volume = {{61}}, + author = {Lu, Yongjun and Weers, Brock and Stellwagen, Nancy C.} } @article{Laurens2009, year = {2009}, - title = {Dissecting protein-induced {DNA} looping dynamics in real time}, - journal = {Nucleic Acids Research}, - author = {Laurens, N. and Bellamy, S.R.W. and Harms, A.F. and Kovacheva, Y.S. and Halford, St.F. and Wuite, G.J.L.} + title = {{Dissecting protein-induced DNA looping dynamics in real time}}, + journal = {{Nucleic Acids Research}}, + 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.} } @article{Yguerabide1998b, @@ -16450,16 +16449,16 @@ @article{Strick1998, year = {1998}, - title = {Behavior of Supercoiled {DNA}}, - pages = {2016-2028}, - journal = {Biophysical Journal}, - volume = {74}, + title = {{Behavior of Supercoiled DNA}}, + pages = {{2016-2028}}, + journal = {{Biophysical Journal}}, + volume = {{74}}, author = {Strick, T.R. and Allemand, J.-F. and Bensimon, D. and Croquette, V.} } @article{Pouget2004, - number = {9}, + number = {{9}}, year = {2004}, - title = {Single-particle tracking for {DNA} tether length monitoring}, - journal = {Nucleic Acids Research}, - volume = {32}, + title = {{Single-particle tracking for DNA tether length monitoring}}, + journal = {{Nucleic Acids Research}}, + volume = {{32}}, author = {Pouget, Noelle and Dennis, Cynthia and Turlan, Catherine and Grigoriev, Mikhail and Chandler, Michael and Salome, Laurence} } @@ -16467,26 +16466,26 @@ number = {{1}}, year = {1967}, - title = {The Statistical Mechanical Theory of Stiff Chains}, - pages = {219-226}, - journal = {Journal of the Physical Society of Japan}, - volume = {22}, + title = {{The Statistical Mechanical Theory of Stiff Chains}}, + pages = {{219-226}}, + journal = {{Journal of the Physical Society of Japan}}, + volume = {{22}}, author = {Saito, Nobuhiko and Takahashi, Kunihiko and Yunoki, Yasuo} } @article{Smith1996, - number = {5250}, + number = {{5250}}, year = {1996}, - title = {{Overstretching B-DNA}: The Elastic Response of Individual Double-Stranded and Single-Stranded {DNA} Molecules}, - pages = {795-799}, + title = {{Overstretching B-DNA: The Elastic Response of Individual Double-Stranded and Single-Stranded DNA Molecules}}, + pages = {{795-799}}, journal = {{Science}}, - volume = {271}, + volume = {{271}}, author = {Smith, Steven B. and Cui, Yujia and Bustamante, Carlos} } @article{Roeffaers2007, - number = {31}, + number = {{31}}, year = {2007}, - title = {Single-molecule fluorescence spectroscopy in (bio)catalysis}, - pages = {12603-12609}, - journal = {Proceedings of the National Academy of Sciences of the USA}, - volume = {104}, + title = {{Single-molecule fluorescence spectroscopy in (bio)catalysis}}, + pages = {{12603-12609}}, + journal = {{Proceedings of the National Academy of Sciences of the USA}}, + volume = {{104}}, 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} } @@ -16646,20 +16645,20 @@ journal = {{Current Opinion in Structural Biology}}, volume = {{10}}, - author = {Bustamante, C.and Smith, S.B. and Liphardt, Jan and Smith, Doug} + author = {Bustamante, Carlos and Smith, Steven B. and Liphardt, Jan and Smith, Doug} } @article{Bustamante2003, year = {2003}, - title = {Ten years of tension: single-molecule {DNA} mechanics}, - pages = {423-427}, - journal = {Nature}, - volume = {421}, - author = {Bustamante, C. and Bryant, Zev and Smith, S.B.} + title = {{Ten years of tension: single-molecule DNA mechanics}}, + pages = {{423-427}}, + journal = {{Nature}}, + volume = {{421}}, + author = {Bustamante, Carlos and Bryant, Zev and Smith, Steven B.} } @article{Holtzer2007, year = {2007}, - title = {Nanometric three-dimensional tracking of individual quantom dots in cells}, - pages = {053902}, - journal = {Applied Physics Letters}, - volume = {90}, + title = {{Nanometric three-dimensional tracking of individual quantom dots in cells}}, + pages = {{053902}}, + journal = {{Applied Physics Letters}}, + volume = {{90}}, author = {Holtzer, L. and Meckel, T. and Schmidt, T.} } @@ -16674,26 +16673,26 @@ @article{Lindner2009, year = {2009}, - title = {Studies of Single Molecules in their Natural Form}, - pages = {283-291}, - journal = {Israel Journal of Chemistry}, - volume = {49}, + title = {{Studies of Single Molecules in their Natural Form}}, + pages = {{283-291}}, + journal = {{Israel Journal of Chemistry}}, + volume = {{49}}, author = {Lindner, Moshe and Nir, Guy and Dietrich, Heidelinde R. 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I. Qualitative Model}}, + pages = {{1178-1191}}, + journal = {{Biophysical Journal}}, + volume = {{92}}, + author = {Saxton, Michael J.} } @article{Otto1994, - number = {3}, + number = {{3}}, year = {1994}, - title = {Persistence lengths of semiflexible chains - Methods and approximations}, - pages = {543-555}, - journal = {Macromolecular Theory and Simulations}, - volume = {3}, + title = {{Persistence lengths of semiflexible chains - Methods and approximations}}, + pages = {{543-555}}, + journal = {{Macromolecular Theory and Simulations}}, + volume = {{3}}, author = {Otto, Matthias and Eckert, Jochen and Vilgis, Thomas A.} } @article{Vennemann2007, - number = {3}, + number = {{3}}, year = {2007}, - title = {In vivo whole-field blood velocity measurement techniques}, - pages = {495-511}, - journal = {Experiments in Fluids}, - volume = {42}, + title = {{In vivo whole-field blood velocity measurement techniques}}, + pages = {{495-511}}, + journal = {{Experiments in Fluids}}, + volume = {{42}}, author = {Vennemann, Peter and Lindken, Ralph and Westerweel, Jerry} } @article{Vosch2007, - number = {31}, + number = {{31}}, year = {2007}, - title = {Strongly emissive individual DNA-encapsulated Ag nanoclusters as single-molecule fluorophores}, - pages = {12616-12621}, - journal = {Proceedings of the National Academy of Sciences of the USA}, - volume = {104}, + title = {{Strongly emissive individual DNA-encapsulated Ag nanoclusters as single-molecule fluorophores}}, + pages = {{12616-12621}}, + journal = {{Proceedings of the National Academy of Sciences of the USA}}, + volume = {{104}}, author = {Vosch, Tom and Antoku, Yasuko and Hsiang, Jung-Cheng and Richards, Chris I. and Gonzalez, Jose I. and Dickson, Robert M.} } @@ -16831,10 +16830,10 @@ } @article{Singh-Zocchi2003, - number = {13}, + number = {{13}}, year = {2003}, - title = {Single-molecule detection of {DNA} hybridization}, - pages = {7605-7610}, - journal = {Proceedings of the National Academy of Sciences of the USA}, - volume = {100}, + title = {{Single-molecule detection of DNA hybridization}}, + pages = {{7605-7610}}, + journal = {{Proceedings of the National Academy of Sciences of the USA}}, + volume = {{100}}, author = {Singh-Zocchi, Mukta and Dixit, Sanhita and Ivanov, Vassili and Zocchi, Giovanni} } @@ -16948,28 +16947,28 @@ } @article{Kao1994, - number = {3}, + number = {{3}}, year = {1994}, - title = {Tracking of single fluorescent particles in three dimensions: use of cylindrical optics to encode particle position}, - pages = {1291-1300}, - journal = {Biophysical Journal}, - volume = {67}, + title = {{Tracking of single fluorescent particles in three dimensions: use of cylindrical optics to encode particle position}}, + pages = {{1291-1300}}, + journal = {{Biophysical Journal}}, + volume = {{67}}, author = {Kao, H.P. and Verkman, A.S.} } @article{Jo2007, - number = {8}, + number = {{8}}, year = {2007}, - title = {A single-molecule barcoding system using nanoslits for {DNA} analysis}, - pages = {2673-2678}, - journal = {Proceedings of the National Academy of Sciences of the USA}, - volume = {104}, + title = {{A single-molecule barcoding system using nanoslits for DNA analysis}}, + pages = {{2673-2678}}, + journal = {{Proceedings of the National Academy of Sciences of the USA}}, + volume = {{104}}, 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.} } @article{Speidel2003, - number = {2}, + number = {{2}}, year = {2003}, - title = {Three-dimensional tracking of fluorescent nanoparticles with subnanometer precision by use of off-focus imaging}, - pages = {69-71}, - journal = {Optics Letters}, - volume = {28}, + title = {{Three-dimensional tracking of fluorescent nanoparticles with subnanometer precision by use of off-focus imaging}}, + pages = {{69-71}}, + journal = {{Optics Letters}}, + volume = {{28}}, author = {Speidel, Michael and Jonas, Alexandr and Florin, Ernst-Ludwig} } @@ -16994,9 +16993,9 @@ @article{Willert1992, year = {1992}, - title = {Three-dimensional particle imaging with a single camera}, - pages = {353-358}, - journal = {Experiments in Fluids}, - volume = {12}, - author = {Willert, C.E. and Gharib, M.} + title = {{Three-dimensional particle imaging with a single camera}}, + pages = {{353-358}}, + journal = {{Experiments in Fluids}}, + volume = {{12}}, + author = {Willert, C. E. and Gharib, M.} } @article{Oberholzer1997, @@ -17007,20 +17006,20 @@ journal = {Journal of Chemical Physics}, volume = {107}, - author = {Oberholzer, M.R. and Wagner, Norman J. and Lenhoff, A.M.} + author = {Oberholzer, M.R. and Wagner, N.J. and Lenhoff, Abraham M.} } @article{Wiggins2006, year = {2006}, - title = {Generalized theory of semiflexible polymers}, - journal = {Physical Review E}, - volume = {73}, - author = {Wiggins, P.A. and Nelson, P.C.} + title = {{Generalized theory of semiflexible polymers}}, + journal = {{Physical Review E}}, + volume = {{73}}, + author = {Wiggins, Paul A. and Nelson, Philip C.} } @article{Brenner1961, - number = {3-4}, + number = {{3-4}}, year = {1961}, - title = {The slow motion of a sphere through a viscous fluid towards a plane surface}, - pages = {242-251}, - journal = {Chemical Engineering Science}, - volume = {16}, + title = {{The slow motion of a sphere through a viscous fluid towards a plane surface}}, + pages = {{242-251}}, + journal = {{Chemical Engineering Science}}, + volume = {{16}}, author = {Brenner, Howard} } @@ -17187,15 +17186,15 @@ month = {October 1, 2006}, year = {2006}, - title = {Elementary simulation of tethered Brownian motion}, - author = {Beausang, J.F. and Zurla, Chiara and Sullivan, Luke and Finzi, Laura and Nelson, P.C.} + title = {{Elementary simulation of tethered Brownian motion}}, + author = {Beausang, John F. and Zurla, Chiara and Sullivan, Luke and Finzi, Laura and Nelson, Philip C.} } @article{Beausang2007, - number = {6}, + number = {{6}}, year = {2007}, - title = {Elementary simulation of tethered Brownian motion}, - pages = {20-523}, - journal = {American Journal of Physics}, - volume = {75}, - author = {Beausang, J.F. and Zurla, Chiara and Finzi, Laura and Sullivan, Luke and Nelson, P.C.} + title = {{Elementary simulation of tethered Brownian motion}}, + pages = {{520-523}}, + journal = {{American Journal of Physics}}, + volume = {{75}}, + author = {Beausang, John F. and Zurla, Chiara and Finzi, Laura and Sullivan, Luke and Nelson, Philip C.} } @phdthesis{Guasto2008, @@ -17313,34 +17312,34 @@ @article{Bouchiat1999, year = {1999}, - title = {Estimating the Persistence Length of a Worm-Like Chain Molecule from Force-Extension Measurements}, - pages = {409-413}, - journal = {Biophysical Journal}, - volume = {76}, - author = {Bouchiat, C. and Wang, M.D. and Allemand, J.-F. and Strick, T. and Block, S.M. and Croquette, V.} + title = {{Estimating the Persistence Length of a Worm-Like Chain Molecule from Force-Extension Measurements}}, + pages = {{409-413}}, + journal = {{Biophysical Journal}}, + volume = {{76}}, + author = {Bouchiat, C. and Wang, M. D. and Allemand, J.-F. and Strick, T. and Block, S. M. and Croquette, V.} } @article{Cady2007, year = {2007}, - title = {Optimized linkage and quenching strategies for quantum dot molecular beacons}, - pages = {116-124}, - journal = {Molecular and Cellular Probes}, - volume = {21}, + title = {{Optimized linkage and quenching strategies for quantum dot molecular beacons}}, + pages = {{116-124}}, + journal = {{Molecular and Cellular Probes}}, + volume = {{21}}, author = {Cady, Nathaniel C. and Strickland, Aaron D. and Batt, Carl A.} } @article{Fraden1993, - number = {4}, + number = {{4}}, year = {1993}, - title = {Angular correlations and the isotropic-nematic phase transition in suspensions of tobacco mosaic virus}, - pages = {2816-2838}, - journal = {Physical Review E}, - volume = {48}, + title = {{Angular correlations and the isotropic-nematic phase transition in suspensions of tobacco mosaic virus}}, + pages = {{2816-2838}}, + journal = {{Physical Review E}}, + volume = {{48}}, author = {Fraden, Seth and Maret, Georg} } @article{Bustamante1994, - number = {5178}, + number = {{5178}}, year = {1994}, - title = {Entropic Elasticity of lambda-Phage DNA}, - pages = {1599-1601}, - journal = {Science}, - volume = {265}, + title = {{Entropic Elasticity of lambda-Phage DNA}}, + pages = {{1599-1601}}, + journal = {{Science}}, + volume = {{265}}, author = {Bustamante, C. and Marko, J.F. and Siggia, E.D. and Smith, S.} } @@ -17365,25 +17364,25 @@ @article{Lambert2006, year = {2006}, - title = {{Mg2+-}Induced Compaction of Single RNA Molecules Monitored by Tethered Particle Microscopy}, - pages = {3672-3685}, - journal = {Biophysical Journal}, - volume = {90}, - author = {Lambert, M.N. and {V\"ocker}, E. and Blumberg, S. and Redemann, S. and Gajraj, A. and Meiners, J.-C. and Walter, N.G.} + title = {{Mg2+-Induced Compaction of Single RNA Molecules Monitored by Tethered Particle Microscopy}}, + pages = {{3672-3685}}, + journal = {{Biophysical Journal}}, + volume = {{90}}, + 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.} } @article{Kessler2004, - number = {2}, + number = {{2}}, year = {2004}, - title = {Distribution functions for filaments under tension}, - pages = {1155-1164}, - journal = {Journal of Chemical Physics}, - volume = {121}, + title = {{Distribution functions for filaments under tension}}, + pages = {{1155-1164}}, + journal = {{Journal of Chemical Physics}}, + volume = {{121}}, author = {Kessler, David A. and Rabin, Yitzhak} } @article{Edwards1970, year = {1970}, - title = {Theory of the Single Chain}, - pages = {43}, - journal = {Discussions of the Faraday Society}, - volume = {49}, + title = {{Theory of the Single Chain}}, + pages = {{43}}, + journal = {{Discussions of the Faraday Society}}, + volume = {{49}}, author = {Edwards, S.F.} } @@ -18468,5 +18467,7 @@ @article{Manghi2010, year = {2010}, - title = {Probing {DNA} conformational changes with high temporal resolution by tethered particle motion}, + title = {Probing {DNA} conformational changes +with high temporal resolution by tethered +particle motion}, pages = {046003}, journal = {Physical Biology}, @@ -18726,8 +18727,10 @@ @article{Karuppasamy2011, year = {2011}, - title = {Radiation Damage Studies in Single Particle Cryo-ElectronMicroscopy}, - note = {accepted}, + title = {Radiation damage in single-particle cryo-electron +microscopy: effects of dose and dose rate}, + pages = {398-412}, journal = {Journal of Synchrotron Radiation}, - author = {Karuppasamy, M. and Nejadasl, F.K. and Vulovic, M. and Koster, A.J. and Ravelli, R.B.G. } + volume = {18}, + author = {Karuppasamy, M. and Karimi Nejadasl, F and Vulovic, M. and Koster, A.J. and Ravelli, R.B.G. } } @article{Krysting2011, @@ -18769,5 +18772,5 @@ number = {5196}, year = {1995}, - title = {Measurement of Lactose Repressor-Mediated Loop Formation and Breakdown in Single {DNA} Molecules}, + title = {Measurement of Lactose Repressor-Mediated Loop Formation and Breakdown in Single DNA Molecules}, pages = {378-380}, journal = {Science}, @@ -18846,5 +18849,5 @@ journal = {Journal of Chemical Physics}, volume = {113}, - author = {Bevan, M.A. and Prieve, D.C.} + author = {Bevan, Michael A. and Prieve, Dennis C.} } @article{Stallinga2005a, @@ -18863,5 +18866,5 @@ journal = {Biophysical Journal}, volume = {96}, - author = {Fan, H.-F. and Li, H.-W.} + author = {Fan, Hsiu-Fang and Li, Hung-Wen} } @article{Geggier2010, @@ -18881,5 +18884,5 @@ journal = {Macromolecules}, volume = {29}, - author = {Smith, D.E. and Perkins, T.T. and Chu, S.} + author = {Smith, Douglas E. and Perkins, Thomas T. and Chu, Steven} } @article{Hodgson1991, @@ -18890,5 +18893,5 @@ journal = {Journal of Chemical Physics}, volume = {95}, - author = {Hodgson, D.F. and Amis, E.J.} + author = {Hodgson, Donald F. and Amis, Eric J.} } @inproceedings{Rieger2011, @@ -18910,4 +18913,393 @@ address = {New York}, publisher = {John Wiley \& Sons, Inc}, - author = {Munson, B.R. and Young, D.F. and Okiishi, T.H.} -} + author = {Munson, Bruce R. and Young, Donald F. and Okiishi, Theodore H.} +} +@article{Rosenthal2003, + number = {4}, + year = {2003}, + title = {Optimal Determination of Particle Orientation, +Absolute Hand, and Contrast Loss in Single-particle Electron Cryomicroscopy}, + pages = {721-745}, + journal = {Journal of Molecular Biology}, + volume = {333}, + author = {Rosenthal, P.B. and Henderson, R.} +} +@article{Wicker2009, + number = {18}, + year = {2009}, + title = {Characterisation of a resolution enhancing image inversion interferometer}, + pages = {15491-15501}, + journal = {Optics Express}, + volume = {17}, + author = {Wicker, K. and Sindbert, S. and Heintzmann, R.} +} +@article{Wicker2007, + number = {19}, + year = {2007}, + title = {Interferometric resolution improvement for confocal microscopes}, + pages = {12206-12216}, + journal = {Optics Express}, + volume = {15}, + author = {Wicker, K. and Heintzmann, R.} +} +@article{Schermelleh2010, + number = {2}, + year = {2010}, + title = {A guide to super-resolution fluorescence microscopy}, + pages = {165-175}, + journal = {The journal of cell biology}, + volume = {190}, + author = {Schermelleh, L. and Heintzmann, R. and Leonhardt, H.} +} +@article{Ruckstuhl2004, + number = {18}, + year = {2004}, + title = {Supercritical angle fluorescence {(SAF)} microscopy}, + pages = {4246-4254}, + journal = {Optics Express}, + volume = {12}, + author = {Ruckstuhl, T. and Verdes, D.} +} +@article{Rohrbach2009, + number = {19}, + year = {2009}, + title = {Artifacts resulting from imaging in scattering media: a theoretical prediction}, + pages = {3041-3043}, + journal = {Optics Letters}, + volume = {34}, + author = {Rohrbach, A.} +} +@article{Murdy2010, + year = {2010}, + title = {Isotropic Diffraction-Limited Focusing Using a Single Objective Lens}, + pages = {203903}, + journal = {Physical Review Letters}, + volume = {105}, + author = {Murdy, E. and Moral, E. le and Ferrand, P. and Chaumet, P.C. and Sentenac, A. } +} +@article{Min2009, + number = {22}, + year = {2009}, + title = {Imaging chromophores with undetectable fluorescence by stimulated emission microscopy}, + pages = {1105-1109}, + journal = {Nature}, + volume = {461}, + author = {Min, W. and Lu, S. and Chong, S. and Roy, R. and Holtom, G.R. and Xie, X.S.} +} +@inbook{Manley2010, + series = {Methods in Enzymology}, + year = {2010}, + title = {Single-Particle Tracking Photoactivated Localization +Microscopy for Mapping Single-Molecule Dynamics}, + pages = {109-120}, + volume = {475}, + chapter = {5}, + publisher = {Elsevier}, + author = {Manely, S. and Gillette, J.M. and Lippincott-Schwartz, J.} +} +@article{Luisier2007, + number = {3}, + year = {2007}, + title = {A New {SURE} Approach to Image Denoising: +Interscale Orthonormal Wavelet Thresholding}, + pages = {593-606}, + journal = {IEEE Transactions on Image Processing}, + volume = {16}, + author = {Luisier, F. and Blu, T. and Unser, M.} +} +@article{Krizek2011, + number = {4}, + year = {2011}, + title = {Minimizing detection errors in single molecule localization microscopy}, + pages = {3226-3235}, + journal = {Optics Express}, + volume = {19}, + author = {Krizek, P. and Raska, I. and Hagen, G.M} +} +@article{Kaufmann2011a, + year = {2011}, + title = {Imaging label-free intracellular structures by localisation microscopy}, + pages = {348-352}, + journal = {Micron}, + volume = {42}, + author = {Kaufmann, R. and {M\"uller}, P. and Hausmann, M. and Cremer, C.} +} +@article{Kaufmann2011, + number = {1}, + year = {2011}, + title = {Analysis of {Her2/neu} membrane protein clusters in different types of breast cancer cells using localization microscopy}, + pages = {46-54}, + journal = {Journal of Microscopy}, + volume = {242}, + author = {Kaufmann, R. and {M\"uller}, P. and Hildenbrand, G. and Hausmann, M. and Cremer, C.} +} +@article{Fujita2007, + year = {2007}, + title = {High-Resolution Confocal Microscopy by Saturated Excitation of Fluorescence}, + pages = {228105}, + journal = {Physical Review Letters}, + volume = {99}, + author = {Fujita, K. and Kobayashi, M. and Kawano, S. and YTamanaka, M. and Kawata, S.} +} +@article{Fahrbach2010, + year = {2010}, + title = {Microscopy with self-reconstructing beams}, + note = {DOI: 10.1038/NPHOTON.2010.204}, + journal = {Nature photonics}, + author = {Fahrbach, F.O. and Simon, P. and Rohrbach, A.} +} +@article{Debarre2007, + number = {13}, + year = {2007}, + title = {Image based adaptive optics through optimisation of low spatial frequencies}, + pages = {8176-8190}, + journal = {Optics Express}, + volume = {15}, + author = {Debarre, D. and Booth, M.J. and Wilson, T.} +} +@article{Cox2004, + year = {2004}, + title = {Practical Limits of Resolution in Confocal and Non-Linear Microscopy}, + pages = {18-22}, + journal = {MICROSCOPY RESEARCH AND TECHNIQUE}, + volume = {63}, + author = {Cox, G. and Sheppard, C.J.R.} +} +@article{Cox1982, + number = {5}, + year = {1982}, + title = {Improvement in resolution by nearly confocal microscopy}, + pages = {778-781}, + journal = {Applied Optics}, + volume = {21}, + author = {Cox, I.J. and Sheppard, C.J.R. and Wilson, T.} +} +@article{Dobrucki2007, + year = {2007}, + title = {Scattering of Exciting Light by Live Cells in Fluorescence Confocal Imaging: Phototoxic Effects and Relevance for {FRAP} Studies}, + pages = {1778-1786}, + journal = {Biophysical Journal}, + volume = {93}, + author = {Dobrucki, J.W. and Feret, D. and Noatynska, A.} +} +@phdthesis{Wicker2010, + month = {October}, + year = {2010}, + title = {Increasing resolution and light efficiency +in fluorescence microscopy}, + address = {United Kingdom}, + school = {King's College London}, + author = {Wicker, K.} +} +@article{PoissonNoise, + number = {1}, + year = {1965}, + title = {Noise in Photoemission Current}, + pages = {79-80}, + journal = {Applied Optics}, + volume = {4}, + author = {Fried, D.L.} +} +@article{Kiel2007, + year = {2007}, + title = {Direct Monitoring of Formation and Dissociation of Individual Metal Complexes by Single-Molecule Fluorescence Spectroscopy}, + pages = {3363-3366}, + journal = {Angewandte Chemie Interational Edition}, + volume = {46}, + author = {Kiel, A. and Kovacs, J. and Mokhir, A. and {Kr\"amer}, R. and Herten, D.-P.} +} +@article{Schwering2011, + year = {2011}, + title = {Far-Field Nanoscopy with Reversible Chemical Reactions}, + pages = {2940-2945}, + journal = {Angewandte Chemie International Edition}, + volume = {50}, + author = {Schwering, M. and Kiel, A. and Kurz, A. and Lymperopoulos,K. and {Spr\"odefeld}, A. and {Kr\"amer}, R. and Herten, D.-P. } +} +@article{Rossow2010, + number = {11}, + year = {2010}, + title = {Raster image correlation spectroscopy in live cells}, + pages = {1761-1773}, + journal = {Nature Protocols}, + volume = {5}, + author = {Rossow, M.J. and Sasaki, J.M. and Digmann, M.A. and Gratton, E.} +} +@inproceedings{Knutsson1987, + month = {September}, + year = {1987}, + title = {A tensor representation of 3-D structure}, + booktitle = {5th IEEE-ASSP and EURASIP Workshop on 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title = {Generalized Hard Constraints for Graph +Segmentation}, + booktitle = {Image Analysis}, + pages = {36-47}, + editor = {Heyden, A. and Kahl, F.}, + address = {Heidelberg}, + publisher = {Springer}, + author = {Malmberg, F. and Strand, R. and {Nystr\"om}, I.} +} +@inproceedings{Larsson2011, + series = {Lecture Notes in Computer Science 6688}, + year = {2011}, + title = {Using Fourier Descriptors and Spatial Models +for Traffic Sign Recognition}, + booktitle = {Image Analysis}, + pages = {238-249}, + editor = {Heyden, A. and Kahl, F.}, + address = {Heidelberg}, + publisher = {Springer}, + author = {Larsson, F. and Felsberg, M.} +} +@inproceedings{Landstrom2011, + series = {Lecture Notes in Computer Science 6688}, + year = {2011}, + title = {Image Reconstruction by Prioritized +Incremental Normalized Convolution}, + booktitle = {Image Analysis}, + pages = {176-185}, + editor = {Heyden, A. and Kahl, F.}, + address = {Heidelberg}, + publisher = {Springer}, + author = {{Landstr\"om}, A. and Nellros, F. and Jonsson, H. and Thurley, M.} +} +@inproceedings{Knutsson2011, + series = {Lecture Notes in Computer Science 6688}, + year = {2011}, + title = {Representing Local Structure Using Tensors {II}}, + booktitle = {Image Analysis}, + pages = {545-556}, + editor = {Heyden, A. and Kahl, F.}, + address = {Heidelberg}, + publisher = {Springer}, + author = {Knutsson, H. and Westin, C.-F. and Andersson, M.} +} +@inproceedings{Josth2011, + series = {Lecture Notes in Computer Science 6688}, + year = {2011}, + title = {Real-Time Line Detection Using Accelerated +High-Resolution Hough Transform}, + booktitle = {Image Analysis}, + pages = {784-793}, + editor = {Heyden, A. and Kahl, F.}, + address = {Heidelberg}, + publisher = {Springer}, + author = {Josth, R. and Dubska, M. and Herout, A. and Havel, J.} +} +@inproceedings{Eklund2011, + series = {Lecture Notes in Computer Science 6688}, + year = {2011}, + title = {Using the Local Phase of the Magnitude of the +Local Structure Tensor for Image Registration}, + booktitle = {Image Analysis}, + pages = {414-423}, + editor = {Heyden, A. and Kahl, F.}, + address = {Heidelberg}, + publisher = {Springer}, + author = {Eklund, A. and Forsberg, D. and Andersson, M. and Knutsson, H.} +} +@inproceedings{Astrom2011, + series = {Lecture Notes in Computer Science 6688}, + year = {2011}, + title = {Color Persistent Anisotropic Diffusion of Images}, + booktitle = {Image Analysis}, + pages = {262-272}, + editor = {Heyden, A. and Kahl, F.}, + address = {Heidelberg}, + publisher = {Springer}, + author = {{\AAstr\"om}, F. and Felsberg, M. and Lenz, R.} +} +@article{Unser2009, + number = {11}, + year = {2011}, + title = {Multiresolution Monogenic Signal Analysis Using +the {Riesz-Laplace} Wavelet Transform}, + pages = {2402-2418}, + journal = {IEEE TRANSACTIONS ON IMAGE PROCESSING}, + volume = {18}, + author = {Unser, M. and Sage, D. and van de Ville, D.} +} +@article{Frank1976, + year = {1975}, + title = {Signal to noise ratio of electron micrographs obtained by cross correlation}, + pages = {376-379}, + journal = {Nature}, + volume = {256}, + author = {Frank, J. and Al-Ali, L.} +} +@article{Patra2005, + year = {2005}, + title = {Defocused imaging of quantum-dot angular distribution of radiation}, + pages = {101103}, + journal = {Applied Physics Letters}, + volume = {87}, + author = {Patra, D. and Gergor, I. and Enderlein, J.} +} +@article{Toprak2006, + number = {17}, + year = {2006}, + title = {Defocused orientation and position imaging +{(DOPI)} of myosin {V}}, + pages = {6495-6499}, + journal = {Proceedings of the National Academy of Sciences USA}, + volume = {103}, + author = {Toprak, E. and Enderlein, J. and Syed, S. and McKinney, S.A. and Petschek, R.G. and Ha, T. and Goldman, Y.E. and Selvin, P.R.} +} +@article{Geissbuehler2011, + number = {3}, + year = {2011}, + title = {Comparison between {SOFI} and {STORM}}, + pages = {408-420}, + journal = {BIOMEDICAL OPTICS EXPRESS}, + volume = {2}, + author = {Geissbuehler, S. and Dellagiacoma, C. and Lasser, T.} +} +@article{Enderlein2005, + year = {2005}, + title = {Performance of Fluorescence Correlation +Spectroscopy for Measuring Diffusion and +Concentration}, + pages = {2324-2336}, + journal = {ChemPhysChem}, + volume = {6}, + author = {Enderlein, J. and Gregor, I. and Patra, D. and Dertinger, T. and Kaupp, U.B.} +} +@article{Dertinger2007, + year = {2007}, + title = {Two-Focus Fluorescence Correlation +Spectroscopy: A New Tool for Accurate and +Absolute Diffusion Measurements}, + pages = {433-443}, + journal = {ChemPhysChem}, + volume = {8}, + author = {Dertinger, T. and Pacheco, V. and Hocht, I. van der and Hartmann, R. and Gregor, I. and Enderlein, J.} +} Index: /qipapers.html =================================================================== --- /qipapers.html (revision 266) +++ /qipapers.html (revision 267) @@ -14,5 +14,5 @@ (see http://www.lri.fr/~filliatr/bibtex2html/), with the following command: - /usr/bin/bibtex2html -o - -t qipapers.html -s plain /tmp/tmpFW7Uc5.bib --> + /usr/bin/bibtex2html -o - -t qipapers.html -s plain /tmp/tmpZPvuD7.bib -->

qipapers.html

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Lenhoff. - Grand canonical Brownian dynamics simulation of colloidal - adsorption. +M.R. Oberholzer, N.J. Wagner, and Abraham M. Lenhoff. + Grand canonical brownian dynamics simulation of colloidal adsorption. Journal of Chemical Physics, 107(21):9157-9167, 1997. @@ -30805,8 +30803,8 @@ -M. Karuppasamy, F.K. Nejadasl, M. Vulovic, A.J. Koster, and R.B.G. Ravelli. - Radiation damage studies in single particle cryo-electronmicroscopy. - Journal of Synchrotron Radiation, 2011. - accepted. +M. Karuppasamy, F Karimi Nejadasl, M. Vulovic, A.J. Koster, and R.B.G. Ravelli. + Radiation damage in single-particle cryo-electron microscopy: effects + of dose and dose rate. + Journal of Synchrotron Radiation, 18:398-412, 2011. @@ -31103,4 +31101,576 @@ + + + + +[2224] + + +P.B. 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