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@Article{Aragon1976,
  Title                    = {Fluorescence correlation spectroscopy as a probe of molecular dynamics},
  Author                   = {S. R. Aragon and R. Pecora},
  Journal                  = {The Journal of Chemical Physics},
  Year                     = {1976},
  Number                   = {4},
  Pages                    = {1791-1803},
  Volume                   = {64},

  Doi                      = {10.1063/1.432357},
  Owner                    = {paul},
  Publisher                = {AIP},
  Timestamp                = {2012.11.02}
}

@Article{Ashkin1970,
  Title                    = {Acceleration and Trapping of Particles by Radiation Pressure},
  Author                   = {Ashkin, A.},
  Journal                  = {Physical Review Letters},
  Year                     = {1970},

  Month                    = {Jan},
  Pages                    = {156--159},
  Volume                   = {24},

  Doi                      = {10.1103/PhysRevLett.24.156},
  Issue                    = {4},
  Owner                    = {paul},
  Publisher                = {American Physical Society},
  Timestamp                = {2012.11.13}
}

@Article{Axelrod1984,
  Title                    = {Total Internal Reflection Fluorescence},
  Author                   = {Axelrod, D and Burghardt, T P and Thompson, N L},
  Journal                  = {Annual Review of Biophysics and Biomolecular Structure},
  Year                     = {1984},

  Month                    = jun,
  Number                   = {1},
  Pages                    = {247--268},
  Volume                   = {13},

  Booktitle                = {Annual Review of Biophysics and Bioengineering},
  Comment                  = {doi: 10.1146/annurev.bb.13.060184.001335},
  Doi                      = {10.1146/annurev.bb.13.060184.001335},
  ISSN                     = {0084-6589},
  Owner                    = {paul},
  Publisher                = {Annual Reviews},
  Timestamp                = {2012.02.14}
}

@Article{Bacia2006,
  Title                    = {Fluorescence cross-correlation spectroscopy in living cells},
  Author                   = {Bacia, K. and Kim, S. A. and Schwille, P.},
  Journal                  = {Nat Methods},
  Year                     = {2006},
  Number                   = {2},
  Pages                    = {83--9},
  Volume                   = {3},

  Abstract                 = {Cell biologists strive to characterize molecular interactions directly in the intracellular environment. The intrinsic resolution of optical microscopy, however, allows visualization of only coarse subcellular localization. By extracting information from molecular dynamics, fluorescence cross-correlation spectroscopy (FCCS) grants access to processes on a molecular scale, such as diffusion, binding, enzymatic reactions and codiffusion, and has become a valuable tool for studies in living cells. Here we review basic principles of FCCS and focus on seminal applications, including examples of intracellular signaling and trafficking. We consider FCCS in the context of fluorescence resonance energy transfer and multicolor imaging techniques and discuss application strategies and recent technical advances.},
  Doi                      = {10.1038/nmeth822},
  Keywords                 = {Algorithms Animals Biological Transport Diffusion Endocytosis/physiology Enzymes/metabolism Fluorescence Resonance Energy Transfer/methods Humans Laser Scanning Cytometry/instrumentation/*methods Oligonucleotides/metabolism Protein Binding Protein Transport Proteins/metabolism Signal Transduction/physiology Spectrometry, Fluorescence/instrumentation/methods},
  Owner                    = {paul},
  Timestamp                = {2014.01.15}
}

@Article{Bacia2012,
  Title                    = {Correcting for spectral cross-talk in dual-color fluorescence cross-correlation spectroscopy},
  Author                   = {Bacia, K. and Petr\'{a}\v{s}ek, Zden\v{e}k and Schwille, P.},
  Journal                  = {Chemphyschem},
  Year                     = {2012},
  Number                   = {5},
  Pages                    = {1221--31},
  Volume                   = {13},

  Abstract                 = {Dual-color fluorescence cross-correlation spectroscopy (dcFCCS) allows one to quantitatively assess the interactions of mobile molecules labeled with distinct fluorophores. The technique is widely applied to both reconstituted and live-cell biological systems. A major drawback of dcFCCS is the risk of an artifactual false-positive or overestimated cross-correlation amplitude arising from spectral cross-talk. Cross-talk can be reduced or prevented by fast alternating excitation, but the technology is not easily implemented in standard commercial setups. An experimental strategy is devised that does not require specialized hardware and software for recognizing and correcting for cross-talk in standard dcFCCS. The dependence of the cross-talk on particle concentrations and brightnesses is quantitatively confirmed. Moreover, it is straightforward to quantitatively correct for cross-talk using quickly accessible parameters, that is, the measured (apparent) fluorescence count rates and correlation amplitudes. Only the bleed-through ratio needs to be determined in a calibration measurement. Finally, the limitations of cross-talk correction and its influence on experimental error are explored.},
  Doi                      = {10.1002/cphc.201100801},
  Owner                    = {paul},
  Timestamp                = {2014.01.15}
}

@Article{Bag2012,
  Title                    = {Calibration and Limits of Camera-Based Fluorescence Correlation Spectroscopy: A Supported Lipid Bilayer Study},
  Author                   = {Bag, Nirmalya and Sankaran, Jagadish and Paul, Alexandra and Kraut, Rachel S. and Wohland, Thorsten},
  Journal                  = {ChemPhysChem},
  Year                     = {2012},
  Number                   = {11},
  Pages                    = {2784--2794},
  Volume                   = {13},

  Doi                      = {10.1002/cphc.201200032},
  ISSN                     = {1439-7641},
  Keywords                 = {fluorescence spectroscopy, membrane, multiplexing, point spread function, total internal reflection},
  Owner                    = {paul},
  Publisher                = {WILEY-VCH Verlag},
  Timestamp                = {2012.09.20}
}

@Article{Bestvater2010,
  Title                    = {EMCCD-based spectrally resolved fluorescence correlation spectroscopy},
  Author                   = {Felix Bestvater and Zahir Seghiri and Moon Sik Kang and Nadine Gr\"{o}ner and Ji Young Lee and Kang-Bin Im and Malte Wachsmuth},
  Journal                  = {Optics Express},
  Year                     = {2010},

  Month                    = {Nov},
  Number                   = {23},
  Pages                    = {23818--23828},
  Volume                   = {18},

  Abstract                 = {We present an implementation of fluorescence correlation spectroscopy with spectrally resolved detection based on a combined commercial confocal laser scanning/fluorescence correlation spectroscopy microscope. We have replaced the conventional detection scheme by a prism-based spectrometer and an electron-multiplying charge-coupled device camera used to record the photons. This allows us to read out more than 80,000 full spectra per second with a signal-to-noise ratio and a quantum efficiency high enough to allow single photon counting. We can identify up to four spectrally different quantum dots in vitro and demonstrate that spectrally resolved detection can be used to characterize photophysical properties of fluorophores by measuring the spectral dependence of quantum dot fluorescence emission intermittence. Moreover, we can confirm intracellular cross-correlation results as acquired with a conventional setup and show that spectral flexibility can help to optimize the choice of the detection windows.},
  Doi                      = {10.1364/OE.18.023818},
  Keywords                 = {CCD, charge-coupled device; Confocal microscopy; Spectroscopy, fluorescence and luminescence},
  Owner                    = {paul},
  Publisher                = {OSA},
  Timestamp                = {2012.11.07}
}

@Article{Blom2009,
  Title                    = {Triplet-State Investigations of Fluorescent Dyes at Dielectric Interfaces Using Total Internal Reflection Fluorescence Correlation Spectroscopy},
  Author                   = {Blom, Hans and Chmyrov, Andriy and Hassler, Kai and Davis, Lloyd M. and Widengren, Jerker},
  Journal                  = {The Journal of Physical Chemistry A},
  Year                     = {2009},
  Number                   = {19},
  Pages                    = {5554-5566},
  Volume                   = {113},

  Doi                      = {10.1021/jp8110088},
  Owner                    = {paul},
  Timestamp                = {2012.11.02}
}

@Article{Blom2002,
  Title                    = {Parallel Fluorescence Detection of Single Biomolecules in Microarrays by a Diffractive-Optical-Designed 2 x 2 Fan-Out Element},
  Author                   = {Hans Blom and Mathias Johansson and Anna-Sara Hedman and Liselotte Lundberg and Anders Hanning and Sverker H{\aa}rd and Rudolf Rigler},
  Journal                  = {Applied Optics},
  Year                     = {2002},

  Month                    = {Jun},
  Number                   = {16},
  Pages                    = {3336--3342},
  Volume                   = {41},

  Abstract                 = {We have developed a multifocal diffractive-optical fluorescence correlation spectroscopy system for parallel excitation and detection of single tetramethylrhodamine biomolecules in microarrays. Multifocal excitation was made possible through the use of a 2 {\texttimes} 2 fan-out diffractive-optical element with uniform intensity in all foci. Characterization of the 2 {\texttimes} 2 fan-out diffractive-optical element shows formation of almost perfect Gaussian foci of submicrometer lateral diameter, as analyzed by thermal motion of tetramethylrhodamine dye molecules in solution. Results of parallel excitation and detection in a high-density microarray of circular wells show single-biomolecule sensitivity in all four foci simultaneously.},
  Doi                      = {10.1364/AO.41.003336},
  Keywords                 = {Diffractive optics; Confocal microscopy; Fluorescence microscopy; Fluorescence, laser-induced},
  Owner                    = {paul},
  Publisher                = {OSA},
  Timestamp                = {2012.11.07}
}

@Article{Brinkmeier1999,
  Title                    = {Two-beam cross-correlation:  a method to characterize transport phenomena in micrometer-sized structures.},
  Author                   = {M. Brinkmeier and K. Dörre and J. Stephan and M. Eigen},
  Journal                  = {Analytical Chemistry},
  Year                     = {1999},

  Month                    = {Feb},
  Number                   = {3},
  Pages                    = {609--616},
  Volume                   = {71},

  Abstract                 = {To determine flow properties, namely, the velocity and angle of the flow in microstructured channels, an experimental realization based on fluorescence correlation spectroscopy is described. For this purpose, two micrometer-sized spatially separated volume elements have been created. The cross-correlation signal from these has been recorded and evaluated mathematically. In addition to previous results, two-beam cross-correlation allows for fast and easy determination of even small (down to 200 μm/s) flow velocities, as well as simultaneous measurement of diffusion properties of single dye molecules within a rather short detection time of 5-100 s and an error rate of less than 20\%. The spatial flow resolution is around 1-2 μm, limited by the diameter of the volume element. Furthermore, vectorial flow data can be obtained and evaluated. A discussion of the theoretical background and an experimental verification of the theoretical results is performed. The feasibility of fast and easy data processing is shown if the flow time is the only desired information. Possible applications of this precise and simple method are the determination of transportation effects within artificial microstructures for CE and HPLC, fast chemical kinetics, and high-throughput screening.},
  Doi                      = {10.1021/ac980820i},
  Institution              = {Max-Planck-Institut für biophysikalische Chemie, Am Fassberg, D-37077 Göttingen, Germany.},
  Language                 = {eng},
  Medline-pst              = {ppublish},
  Owner                    = {paul},
  Pmid                     = {21662718},
  Timestamp                = {2012.11.07}
}

@Article{Brutzer2012,
  Title                    = {Scanning Evanescent Fields Using a pointlike Light Source and a Nanomechanical DNA Gear},
  Author                   = {Brutzer, Hergen and Schwarz, Friedrich W. and Seidel, Ralf},
  Journal                  = {Nano Letters},
  Year                     = {2012},
  Number                   = {1},
  Pages                    = {473-478},
  Volume                   = {12},

  Doi                      = {10.1021/nl203876w},
  Owner                    = {paul},
  Timestamp                = {2012.08.09}
}

@Article{Buchholz2012,
  Title                    = {FPGA implementation of a 32x32 autocorrelator array for analysis of fast image series},
  Author                   = {Jan Buchholz and Jan Wolfgang Krieger and G\'{a}bor Mocs\'{a}r and Bal\'{a}zs Kreith and Edoardo Charbon and Gy\"{o}rgy V\'{a}mosi and Udo Kebschull and J\"{o}rg Langowski},
  Journal                  = {Optics Express},
  Year                     = {2012},

  Month                    = {Jul},
  Number                   = {16},
  Pages                    = {17767--17782},
  Volume                   = {20},

  Abstract                 = {With the evolving technology in CMOS integration, new classes of 2D-imaging detectors have recently become available. In particular, single photon avalanche diode (SPAD) arrays allow detection of single photons at high acquisition rates (\&\#x02265; 100kfps), which is about two orders of magnitude higher than with currently available cameras. Here we demonstrate the use of a SPAD array for imaging fluorescence correlation spectroscopy (imFCS), a tool to create 2D maps of the dynamics of fluorescent molecules inside living cells. Time-dependent fluorescence fluctuations, due to fluorophores entering and leaving the observed pixels, are evaluated by means of autocorrelation analysis. The multi-\&\#x003C4; correlation algorithm is an appropriate choice, as it does not rely on the full data set to be held in memory. Thus, this algorithm can be efficiently implemented in custom logic. We describe a new implementation for massively parallel multi-\&\#x003C4; correlation hardware. Our current implementation can calculate 1024 correlation functions at a resolution of 10\&\#x003BC;s in real-time and therefore correlate real-time image streams from high speed single photon cameras with thousands of pixels.},
  Doi                      = {10.1364/OE.20.017767},
  Keywords                 = {Detectors; Arrays; Cameras; Correlators ; Fluorescence microscopy; Three-dimensional microscopy; Spectroscopy, fluorescence and luminescence; Avalanche photodiodes (APDs)},
  Owner                    = {paul},
  Publisher                = {OSA},
  Timestamp                = {2012.10.24}
}

@PhdThesis{Burkhardt2010,
  Title                    = {Electron multiplying CCD – based detection in Fluorescence Correlation Spectroscopy and measurements in living zebrafish embryos},
  Author                   = {Burkhardt, Markus},
  School                   = {Biophysics, BIOTEC, Technische Universität Dresden, Tatzberg 47–51, 01307 Dresden, Germany},
  Year                     = {2010},
  Note                     = {\url{http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-61021}},

  Owner                    = {paul},
  Timestamp                = {2012.10.24}
}

@Article{Burkhardt:06,
  Title                    = {Electron multiplying CCD based detection for spatially resolved fluorescence correlation spectroscopy},
  Author                   = {Markus Burkhardt and Petra Schwille},
  Journal                  = {Optics Express},
  Year                     = {2006},

  Month                    = {Jun},
  Number                   = {12},
  Pages                    = {5013--5020},
  Volume                   = {14},

  Abstract                 = {Fluorescence correlation spectroscopy (FCS) is carried out with an electron multiplying CCD (EMCCD). This new strategy is compared to standard detection by an avalanche photo diode showing good agreement with respect to the resulting autocorrelation curves. Applying different readout modes, a time resolution of 20 {\textmu}s can be achieved, which is sufficient to resolve the diffusion of free dye in solution. The advantages of implementing EMCCD cameras in wide-field ultra low light imaging, as well as in multi-spot confocal laser scanning microscopy, can consequently also be exploited for spatially resolved FCS. First proof-of-principle FCS measurements with two excitation volumes demonstrate the advantage of the flexible CCD area detection.},
  Doi                      = {10.1364/OE.14.005013},
  Keywords                 = {CCD, charge-coupled device; Medical optics and biotechnology; Fluorescence, laser-induced},
  Publisher                = {OSA}
}

@Article{Chiantia2006,
  Title                    = {Combined AFM and Two-Focus SFCS Study of Raft-Exhibiting Model Membranes},
  Author                   = {Chiantia , Salvatore and Ries , Jonas and Kahya, Nicoletta and Schwille, Petra},
  Journal                  = {ChemPhysChem},
  Year                     = {2006},
  Number                   = {11},
  Pages                    = {2409--2418},
  Volume                   = {7},

  Doi                      = {10.1002/cphc.200600464},
  ISSN                     = {1439-7641},
  Keywords                 = {fluorescent probes, force measurements, membranes, sphingolipids},
  Owner                    = {paul},
  Publisher                = {WILEY-VCH Verlag},
  Timestamp                = {2012.10.24}
}

@Article{Dertinger2007,
  Title                    = {Two-Focus Fluorescence Correlation Spectroscopy: A New Tool for Accurate and Absolute Diffusion Measurements},
  Author                   = {Dertinger, Thomas and Pacheco, Victor and von der Hocht, Iris and Hartmann, Rudolf and Gregor, Ingo and Enderlein, Jörg},
  Journal                  = {ChemPhysChem},
  Year                     = {2007},
  Number                   = {3},
  Pages                    = {433--443},
  Volume                   = {8},

  Doi                      = {10.1002/cphc.200600638},
  ISSN                     = {1439-7641},
  Keywords                 = {diffusion coefficients, fluorescence spectroscopy, fluorescent dyes, time-resolved spectroscopy},
  Owner                    = {paul},
  Publisher                = {WILEY-VCH Verlag},
  Timestamp                = {2012.02.14}
}

@Article{Einstein1905,
  Title                    = {Über die von der molekularkinetischen Theorie der Wärme geforderte Bewegung von in ruhenden Flüssigkeiten suspendierten Teilchen},
  Author                   = {Einstein, A.},
  Journal                  = {Annalen der Physik},
  Year                     = {1905},
  Number                   = {8},
  Pages                    = {549--560},
  Volume                   = {322},

  Doi                      = {10.1002/andp.19053220806},
  ISSN                     = {1521-3889},
  Owner                    = {paul},
  Publisher                = {WILEY-VCH Verlag},
  Timestamp                = {2012.11.02}
}

@Article{Elson1974,
  Title                    = {Fluorescence correlation spectroscopy. I. Conceptual basis and theory},
  Author                   = {Elson, Elliot L. and Magde, Douglas},
  Journal                  = {Biopolymers},
  Year                     = {1974},
  Number                   = {1},
  Pages                    = {1--27},
  Volume                   = {13},

  Doi                      = {10.1002/bip.1974.360130102},
  ISSN                     = {1097-0282},
  Owner                    = {paul},
  Publisher                = {Wiley Subscription Services, Inc., A Wiley Company},
  Timestamp                = {2012.09.24}
}

@Article{Enderlein1999,
  Title                    = {Highly Efficient Optical Detection of Surface-Generated Fluorescence},
  Author                   = {J\"{o}rg Enderlein and Thomas Ruckstuhl and Stefan Seeger},
  Journal                  = {Applied Optics},
  Year                     = {1999},

  Month                    = {Feb},
  Number                   = {4},
  Pages                    = {724--732},
  Volume                   = {38},

  Abstract                 = {We present a theoretical study of a new highly efficient system for optical light collection, designed for ultrasensitive fluorescence detection of surface-bound molecules. The main core of the system is a paraboloid glass segment acting as a mirror for collecting the fluorescence. A special feature of the system is its ability to sample not only fluorescence that is emitted below the angle of total internal reflection (the critical angle) but also particularly the light above the critical angle. As shown, this is especially advantageous for collecting the fluorescence of surface-bound molecules. A comparison is made with conventional high-aperture microscope objectives. Furthermore, it is shown that the system allows not only for highly efficient light collection but also for confocal imaging of the detection region, which is of great importance for rejecting scattered light in potential applications such as the detection of only a few molecules.},
  Doi                      = {10.1364/AO.38.000724},
  Keywords                 = {Geometric optical design; Microscopy; Detection; Fluorescence microscopy},
  Owner                    = {paul},
  Publisher                = {OSA},
  Timestamp                = {2012.11.02}
}

@Article{Foo2012,
  Title                    = {Factors Affecting the Quantification of Biomolecular Interactions by Fluorescence Cross-Correlation Spectroscopy},
  Author                   = {Foo, Y. H. and Naredi-Rainer, N. and Lamb, D. C. and Ahmed, S. and Wohland, T.},
  Journal                  = {Biophys J},
  Year                     = {2012},
  Number                   = {5},
  Pages                    = {1174--83},
  Volume                   = {102},

  Abstract                 = {Fluorescence cross-correlation spectroscopy (FCCS) is used to determine interactions and dissociation constants (K(d)s) of biomolecules. The determination of a K(d) depends on the accurate measurement of the auto- and cross-correlation function (ACF and CCF) amplitudes. In the case of complete binding, the ratio of the CCF/ACF amplitudes is expected to be 1. However, measurements performed on tandem fluorescent proteins (FPs), in which two different FPs are linked, yield CCF/ACF amplitude ratios of approximately 0.5 or less for different FCCS schemes. We use single wavelength FCCS and pulsed interleaved excitation FCCS to measure various tandem FPs constituted of different red and green FPs and determine the causes for this suboptimal ratio. The main causes for the reduced CCF/ACF amplitude ratio are differences in observation volumes for the different labels, the existence of dark FPs due to maturation problems, photobleaching, and to a lesser extent Forster (or fluorescence) resonance energy transfer between the labels. We deduce the fraction of nonfluorescent proteins for EGFP, mRFP, and mCherry as well as the differences in observation volumes. We use this information to correct FCCS measurements of the interaction of Cdc42, a small Rho-GTPase, with its effector IQGAP1 in live cell measurements to obtain a label-independent value for the K(d).},
  Doi                      = {10.1016/j.bpj.2012.01.040},
  Owner                    = {paul},
  Timestamp                = {2014.01.15}
}

@Article{Hansen1998,
  Title                    = {Measuring Reversible Adsorption Kinetics of Small Molecules at Solid/Liquid Interfaces by Total Internal Reflection Fluorescence Correlation Spectroscopy},
  Author                   = {Hansen, Richard L and Harris, Joel M},
  Journal                  = {Analytical Chemistry},
  Year                     = {1998},
  Number                   = {20},
  Pages                    = {4247--4256},
  Volume                   = {70},

  Doi                      = {10.1021/ac980925l},
  Owner                    = {paul},
  Timestamp                = {2012.02.14}
}

@Article{Hashmi2007,
  Title                    = {Spatially extended FCS for visualizing and quantifying high-speed multiphase flows in microchannels},
  Author                   = {Sara M. Hashmi and Michael Loewenberg and Eric R. Dufresne},
  Journal                  = {Optics Express},
  Year                     = {2007},

  Month                    = {May},
  Number                   = {10},
  Pages                    = {6528--6533},
  Volume                   = {15},

  Abstract                 = {We report the development of spatially extended fluorescence correlation spectroscopy for visualizing and quantifying multiphase flows in microchannels. We employ simultaneous detection with a high-speed camera across the width of the channel, enabling investigation of the dynamics of the flow at short time scales. We take advantage of the flow to scan the sample past the fixed illumination, capturing frames up to 100 KHz. At these rates, we can resolve the motion of sub-micron particles at velocities up to the order of 1 cm/s. We visualize flows with kymographs and quantify velocity profiles by cross-correlations within the focal volume. We demonstrate the efficacy of our approach by measuring the depth-resolved velocity profile of suspensions of sub-micron diameter silica particles flowing up to 1.5 mm/s.},
  Doi                      = {10.1364/OE.15.006528},
  Keywords                 = {Velocimetry; Flow diagnostics; Fluorescence, laser-induced},
  Owner                    = {paul},
  Publisher                = {OSA},
  Timestamp                = {2012.11.07}
}

@Article{Hassler2005,
  Title                    = {High Count Rates with Total Internal Reflection Fluorescence Correlation Spectroscopy},
  Author                   = {Hassler, Kai and Anhut, Tiemo and Rigler, Rudolf and G\"{o}sch, Michael and Lasser, Theo},
  Journal                  = {Biophysical Journal},
  Year                     = {2005},

  Month                    = jan,
  Number                   = {1},
  Pages                    = {L01--L03},
  Volume                   = {88},

  Doi                      = {10.1529/biophysj.104.053884},
  ISSN                     = {0006-3495},
  Owner                    = {paul},
  Publisher                = {Cell Press},
  Refid                    = {S0006-3495(05)73079-4 DOI - 10.1529/biophysj.104.053884},
  Timestamp                = {2012.05.02}
}

@Article{Hassler2005a,
  Title                    = {Total internal reflection fluorescence correlation spectroscopy (TIR-FCS) with low background and high count-rate per molecule},
  Author                   = {Kai Hassler and Marcel Leutenegger and Per Rigler and Ramachandra Rao and Rudolf Rigler and Michael G\"{o}sch and Theo Lasser},
  Journal                  = {Optics Express},
  Year                     = {2005},

  Month                    = {Sep},
  Number                   = {19},
  Pages                    = {7415--7423},
  Volume                   = {13},

  Abstract                 = {We designed a fluorescence correlation spectroscopy (FCS) system for measurements on surfaces. The system consists of an objective-type total internal reflection fluorescence (TIRF) microscopy setup, adapted to measure FCS. Here, the fluorescence exciting evanescent wave is generated by epi-illumination through the periphery of a high NA oil-immersion objective. The main advantages with respect to conventional FCS systems are an improvement in terms of counts per molecule (cpm) and a high signal to background ratio. This is demonstrated by investigating diffusion as well as binding and release of single molecules on a glass surface. Furthermore, the size and shape of the molecule detection efficiency (MDE) function was calculated, using a wave-vectorial approach and taking into account the influence of the dielectric interface on the emission properties of fluorophores.},
  Doi                      = {10.1364/OPEX.13.007415},
  Keywords                 = {Spectroscopy, fluorescence and luminescence; Spectroscopy, surface; Fluorescence, laser-induced},
  Owner                    = {paul},
  Publisher                = {OSA},
  Timestamp                = {2012.09.21}
}

@Article{Haupts1998,
  Title                    = {Dynamics of fluorescence fluctuations in green fluorescent protein observed by fluorescence correlation spectroscopy},
  Author                   = {Haupts, Ulrich and Maiti, Sudipta and Schwille, Petra and Webb, Watt W.},
  Journal                  = {Proceedings of the National Academy of Sciences},
  Year                     = {1998},
  Number                   = {23},
  Pages                    = {13573-13578},
  Volume                   = {95},

  Abstract                 = {We have investigated the pH dependence of the dynamics of conformational fluctuations of green fluorescent protein mutants EGFP (F64L/S65T) and GFP-S65T in small ensembles of molecules in solution by using fluorescence correlation spectroscopy (FCS). FCS utilizes time-resolved measurements of fluctuations in the molecular fluorescence emission for determination of the intrinsic dynamics and thermodynamics of all processes that affect the fluorescence. Fluorescence excitation of a bulk solution of EGFP decreases to zero at low pH (pKa = 5.8) paralleled by a decrease of the absorption at 488 nm and an increase at 400 nm. Protonation of the hydroxyl group of Tyr-66, which is part of the chromophore, induces these changes. When FCS is used the fluctuations in the protonation state of the chromophore are time resolved. The autocorrelation function of fluorescence emission shows contributions from two chemical relaxation processes as well as diffusional concentration fluctuations. The time constant of the fast, pH-dependent chemical process decreases with pH from 300 μs at pH 7 to 45 μs at pH 5, while the time-average fraction of molecules in a nonfluorescent state increases to 80% in the same range. A second, pH-independent, process with a time constant of 340 μs and an associated fraction of 13% nonfluorescent molecules is observed between pH 8 and 11, possibly representing an internal proton transfer process and associated conformational rearrangements. The FCS data provide direct measures of the dynamics and the equilibrium properties of the protonation processes. Thus FCS is a convenient, intrinsically calibrated method for pH measurements in subfemtoliter volumes with nanomolar concentrations of EGFP.},
  Doi                      = {10.1073/pnas.95.23.13573},
  Owner                    = {paul},
  Timestamp                = {2012.11.01}
}

@Article{Haustein2007,
  Title                    = {Fluorescence Correlation Spectroscopy: Novel Variations of an Established Technique},
  Author                   = {Haustein, Elke and Schwille, Petra},
  Journal                  = {Annual Review of Biophysics and Biomolecular Structure},
  Year                     = {2007},
  Number                   = {1},
  Pages                    = {151-169},
  Volume                   = {36},

  Doi                      = {10.1146/annurev.biophys.36.040306.132612},
  Owner                    = {paul},
  Timestamp                = {2012.02.14}
}

@Article{Helmers2003,
  Title                    = {CMOS vs. CCD sensors in speckle interferometry},
  Author                   = {Heinz Helmers and Markus Schellenberg},
  Journal                  = {Optics \& Laser Technology},
  Year                     = {2003},
  Number                   = {8},
  Pages                    = {587 - 595},
  Volume                   = {35},

  Doi                      = {10.1016/S0030-3992(03)00078-1},
  ISSN                     = {0030-3992},
  Keywords                 = {CCD sensors},
  Owner                    = {paul},
  Timestamp                = {2012.10.06}
}

@Article{Holekamp2008,
  Title                    = {Fast Three-Dimensional Fluorescence Imaging of Activity in Neural Populations by Objective-Coupled Planar Illumination Microscopy},
  Author                   = {Terrence F. Holekamp and Diwakar Turaga and Timothy E. Holy},
  Journal                  = {Neuron},
  Year                     = {2008},
  Number                   = {5},
  Pages                    = {661 - 672},
  Volume                   = {57},

  Doi                      = {10.1016/j.neuron.2008.01.011},
  ISSN                     = {0896-6273},
  Keywords                 = {SYSBIO},
  Owner                    = {paul},
  Timestamp                = {2012.11.13}
}

@Article{Humpolickova2006,
  Title                    = {Probing Diffusion Laws within Cellular Membranes by Z-Scan Fluorescence Correlation Spectroscopy},
  Author                   = {Jana Humpol\'{i}\v{c}kov\'{a} and Ellen Gielen and Ale\v{s} Benda and Veronika Fagulova and Jo Vercammen and Martin vandeVen and Martin Hof and Marcel Ameloot and Yves Engelborghs},
  Journal                  = {Biophysical Journal},
  Year                     = {2006},
  Number                   = {3},
  Pages                    = {L23 - L25},
  Volume                   = {91},

  Doi                      = {10.1529/biophysj.106.089474},
  ISSN                     = {0006-3495},
  Owner                    = {paul},
  Timestamp                = {2012.10.25}
}

@Book{Nocedal2006,
  Title                    = {Numerical Optimization},
  Author                   = {Nocedal J. and Wright S J.},
  Publisher                = {Springer Berlin Heidelberg},
  Year                     = {2006},

  Doi                      = {10.1007/978-3-540-35447-5},
  Owner                    = {paul},
  Timestamp                = {2014.03.31}
}

@Article{Jin2004,
  Title                    = {Near-surface velocimetry using evanescent wave illumination},
  Author                   = {Jin, S. and Huang, P. and Park, J. and Yoo, J. Y. and Breuer, K. S.},
  Journal                  = {Experiments in Fluids},
  Year                     = {2004},
  Pages                    = {825-833},
  Volume                   = {37},

  Affiliation              = {School of Mechanical and Aerospace Engineering Seoul National University Seoul 151-742 Korea},
  Doi                      = {10.1007/s00348-004-0870-7},
  ISSN                     = {0723-4864},
  Issue                    = {6},
  Keyword                  = {Technik},
  Owner                    = {paul},
  Publisher                = {Springer Berlin / Heidelberg},
  Timestamp                = {2012.02.14}
}

@Article{Kannan2006,
  Title                    = {Electron Multiplying Charge-Coupled Device Camera Based Fluorescence Correlation Spectroscopy},
  Author                   = {Kannan, Balakrishnan and Har, Jia Yi and Liu, Ping and Maruyama, Ichiro and Ding, Jeak Ling and Wohland, Thorsten},
  Journal                  = {Analytical Chemistry},
  Year                     = {2006},
  Number                   = {10},
  Pages                    = {3444-3451},
  Volume                   = {78},

  Doi                      = {10.1021/ac0600959},
  Owner                    = {paul},
  Timestamp                = {2012.11.07}
}

@Article{Kim2007,
  Title                    = {Fluorescence correlation spectroscopy in living cells},
  Author                   = {Kim, S. A. and Heinze, K. G. and Schwille, P.},
  Journal                  = {Nat Methods},
  Year                     = {2007},
  Number                   = {11},
  Pages                    = {963--73},
  Volume                   = {4},

  Abstract                 = {Fluorescence correlation spectroscopy (FCS) is an ideal analytical tool for studying concentrations, propagation, interactions and internal dynamics of molecules at nanomolar concentrations in living cells. FCS analyzes minute fluorescence-intensity fluctuations about the equilibrium of a small ensemble (<10(3)) of molecules. These fluctuations act like a 'fingerprint' of a molecular species detected when entering and leaving a femtoliter-sized optically defined observation volume created by a focused laser beam. In FCS the fluorescence fluctuations are recorded as a function of time and then statistically analyzed by autocorrelation analysis. The resulting autocorrelation curve yields a measure of self-similarity of the system after a certain time delay, and its amplitude describes the normalized variance of the fluorescence fluctuations. By fitting the curves to an appropriate physical model, this method provides precise information about a multitude of measurement parameters, including diffusion coefficients, local concentration, states of aggregation and molecular interactions. FCS operates in real time with diffraction-limited spatial and sub-microsecond temporal resolution. Assessing diverse molecular dynamics within the living cell is a challenge well met by FCS because of its single-molecule sensitivity and high dynamic resolution. For these same reasons, however, intracellular FCS measurements also harbor the large risk of collecting artifacts and thus producing erroneous data. Here we provide a step-by-step guide to the application of FCS to cellular systems, including methods for minimizing artifacts, optimizing measurement conditions and obtaining parameter values in the face of diverse and complex conditions of the living cell. A discussion of advantages and disadvantages of one-photon versus two-photon excitation for FCS is available in Supplementary Methods online.},
  Doi                      = {10.1038/nmeth1104},
  Keywords                 = {Animals Biological Transport Cytophotometry/instrumentation/*methods Eukaryotic Cells/*metabolism Fluorescent Dyes/chemistry Humans Kinetics Models, Biological Proteins/chemistry/metabolism Spectrometry, Fluorescence/instrumentation/methods Staining and Labeling},
  Owner                    = {paul},
  Timestamp                = {2014.01.15}
}

@InCollection{Kohl2005,
  Title                    = {Fluorescence Correlation Spectroscopy with Autofluorescent Proteins},
  Author                   = {Kohl, Tobias and Schwille, Petra},
  Booktitle                = {Microscopy Techniques},
  Publisher                = {Springer Berlin / Heidelberg},
  Year                     = {2005},
  Editor                   = {Rietdorf, Jens},
  Pages                    = {1316-1317},
  Series                   = {Advances in Biochemical Engineering/Biotechnology},
  Volume                   = {95},

  Affiliation              = {Pastor-Sander-Bogen 92 37083 Göttingen Germany},
  Doi                      = {10.1007/b102212},
  ISBN                     = {978-3-540-23698-6},
  Keyword                  = {Chemistry and Materials Science},
  Owner                    = {paul},
  Timestamp                = {2012.02.14}
}

@Article{Koppel1974,
  Title                    = {Statistical accuracy in fluorescence correlation spectroscopy},
  Author                   = {Koppel, D.},
  Journal                  = {Phys Rev A},
  Year                     = {1974},
  Pages                    = {1938--1945},
  Volume                   = {10},

  Doi                      = {10.1103/physreva.10.1938},
  Keywords                 = {FCS},
  Owner                    = {paul},
  Timestamp                = {2014.01.15}
}

@Article{Korlach1999,
  Title                    = {Characterization of lipid bilayer phases by confocal microscopy and fluorescence correlation spectroscopy},
  Author                   = {Korlach, J. and Schwille, P. and Webb, W. W. and Feigenson, G. W.},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {1999},
  Number                   = {15},
  Pages                    = {8461--6},
  Volume                   = {96},

  Abstract                 = {We report the application of confocal imaging and fluorescence correlation spectroscopy (FCS) to characterize chemically well-defined lipid bilayer models for biomembranes. Giant unilamellar vesicles of dilauroyl phosphatidylcholine/dipalmitoyl phosphatidylcholine (DLPC/DPPC)/cholesterol were imaged by confocal fluorescence microscopy with two fluorescent probes, 1, 1'-dieicosanyl-3,3,3',3'-tetramethylindocarbocyanine perchlorate (DiI-C(20)) and 2-(4,4-difluoro-5,7-dimethyl-4-bora-3a, 4a-diaza-s-indacene-3-pentanoyl)-1-hexadecanoyl-sn-glycero-3 -phosphoc holine (Bodipy-PC). Phase separation was visualized by differential probe partition into the coexisting phases. Three-dimensional image reconstructions of confocal z-scans through giant unilamellar vesicles reveal the anisotropic morphology of coexisting phase domains on the surface of these vesicles with full two-dimensional resolution. This method demonstrates by direct visualization the exact superposition of like phase domains in apposing monolayers, thus answering a long-standing open question. Cholesterol was found to induce a marked change in the phase boundary shapes of the coexisting phase domains. To further characterize the phases, the translational diffusion coefficient, D(T), of the DiI-C(20) was measured by FCS. D(T) values at approximately 25 degrees C ranged from approximately 3 x 10(-8) cm(2)/s in the fluid phase, to approximately 2 x 10(-9) cm(2)/s in high-cholesterol-content phases, to approximately 2 x 10(-10) cm(2)/s in the spatially ordered phases that coexist with fluid phases. In favorable cases, FCS could distinguish two different values of D(T) in a region of two-phase coexistence on a single vesicle.},
  Doi                      = {10.1073/pnas.96.15.8461},
  Keywords                 = {Carbocyanines Cholesterol/chemistry Diffusion Fluorescent Dyes Lipid Bilayers/*chemistry Liposomes/chemistry Microscopy, Confocal Phospholipids/chemistry Spectrometry, Fluorescence},
  Owner                    = {paul},
  Timestamp                = {2014.01.15}
}

@Article{Korson1969,
  Title                    = {Viscosity of water at various temperatures},
  Author                   = {Korson, Lawrence and Drost-Hansen, Walter and Millero, Frank J.},
  Journal                  = {The Journal of Physical Chemistry},
  Year                     = {1969},
  Number                   = {1},
  Pages                    = {34-39},
  Volume                   = {73},

  Doi                      = {10.1021/j100721a006},
  Owner                    = {paul},
  Timestamp                = {2012.10.29}
}

@Book{LandauLifshitsStatPhys,
  Title                    = {{Statistical Physics, Third Edition, Part 1: Volume 5 (Course of Theoretical Physics, Volume 5)}},
  Author                   = {Landau, L. D. and Lifshitz, E. M.},
  Publisher                = {Butterworth-Heinemann},
  Year                     = {1980},
  Edition                  = {3},
  Month                    = jan,

  Abstract                 = {{A lucid presentation of statistical physics and thermodynamics which develops from the general principles to give a large number of applications of the theory.}},
  Citeulike-article-id     = {1284487},
  Citeulike-linkout-0      = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&amp;path=ASIN/0750633727},
  Citeulike-linkout-1      = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&amp;path=ASIN/0750633727},
  Citeulike-linkout-2      = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&amp;path=ASIN/0750633727},
  Citeulike-linkout-3      = {http://www.amazon.jp/exec/obidos/ASIN/0750633727},
  Citeulike-linkout-4      = {http://www.amazon.co.uk/exec/obidos/ASIN/0750633727/citeulike00-21},
  Citeulike-linkout-5      = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/0750633727},
  Citeulike-linkout-6      = {http://www.worldcat.org/isbn/0750633727},
  Citeulike-linkout-7      = {http://books.google.com/books?vid=ISBN0750633727},
  Citeulike-linkout-8      = {http://www.amazon.com/gp/search?keywords=0750633727\&index=books\&linkCode=qs},
  Citeulike-linkout-9      = {http://www.librarything.com/isbn/0750633727},
  Day                      = {15},
  HowPublished             = {Paperback},
  ISBN                     = {0750633727},
  Keywords                 = {fermi\_statistics, statistical\_physics},
  Owner                    = {paul},
  Posted-at                = {2011-03-03 11:38:41},
  Priority                 = {2},
  Timestamp                = {2012.02.03}
}

@Article{Leutenegger2012,
  Title                    = {Fluorescence correlation spectroscopy with a total internal reflection fluorescence STED microscope (TIRF-STED-FCS)},
  Author                   = {Marcel Leutenegger and Christian Ringemann and Theo Lasser and Stefan W. Hell and Christian Eggeling},
  Journal                  = {Optics Express},
  Year                     = {2012},

  Month                    = {Feb},
  Number                   = {5},
  Pages                    = {5243--5263},
  Volume                   = {20},

  Abstract                 = {We characterize a novel fluorescence microscope which combines the high spatial discrimination of a total internal reflection epi-fluorescence (epi-TIRF) microscope with that of stimulated emission depletion (STED) nanoscopy. This combination of high axial confinement and dynamic-active lateral spatial discrimination of the detected fluorescence emission promises imaging and spectroscopy of the structure and function of cell membranes at the macro-molecular scale. Following a full theoretical description of the sampling volume and the recording of images of fluorescent beads, we exemplify the performance and limitations of the TIRF-STED nanoscope with particular attention to the polarization state of the laser excitation light. We demonstrate fluorescence correlation spectroscopy (FCS) with the TIRF-STED nanoscope by observing the diffusion of dye molecules in aqueous solutions and of fluorescent lipid analogs in supported lipid bilayers in the presence of background signal. The nanoscope reduced the out-of-focus background signal. A lateral resolution down to 40--50 nm was attained which was ultimately limited by the low lateral signal-to-background ratio inherent to the confocal epi-TIRF scheme. Together with the estimated axial confinement of about 55 nm, our TIRF-STED nanoscope achieved an almost isotropic and less than 1 attoliter small all-optically induced measurement volume.},
  Doi                      = {10.1364/OE.20.005243},
  Keywords                 = {Diffraction; Fluorescence microscopy; Fluorescence},
  Owner                    = {paul},
  Publisher                = {OSA},
  Timestamp                = {2012.09.21}
}

@Article{Levenberg1944,
  Title                    = {A method for the solution of certain non-linear problems in least squares},
  Author                   = {Levenberg, Kenneth},
  Journal                  = {Quarterly Journal of Applied Mathmatics},
  Year                     = {1944},
  Number                   = {2},
  Pages                    = {164--168},
  Volume                   = {II},

  __markedentry            = {[paul:6]},
  Citeulike-article-id     = {10796881},
  Keywords                 = {indefinite, nonconvex, optimization},
  Owner                    = {paul},
  Posted-at                = {2012-06-17 09:00:21},
  Priority                 = {2},
  Timestamp                = {2014.03.31}
}

@Article{Lieto2003a,
  Title                    = {Ligand-Receptor Kinetics Measured by Total Internal Reflection with Fluorescence Correlation Spectroscopy},
  Author                   = {Lieto, Alena M. and Cush, Randall C. and Thompson, Nancy L.},
  Journal                  = {Biophysical Journal},
  Year                     = {2003},

  Month                    = nov,
  Number                   = {5},
  Pages                    = {3294--3302},
  Volume                   = {85},

  Doi                      = {10.1016/S0006-3495(03)74748-1},
  ISSN                     = {0006-3495},
  Owner                    = {paul},
  Publisher                = {Cell Press},
  Refid                    = {S0006-3495(03)74748-1 DOI - 10.1016/S0006-3495(03)74748-1},
  Timestamp                = {2012.09.21}
}

@Article{Lieto2003,
  Title                    = {Lateral Diffusion from Ligand Dissociation and Rebinding at Surfaces†},
  Author                   = {Lieto, Alena M. and Lagerholm, B. Christoffer and Thompson, Nancy L.},
  Journal                  = {Langmuir},
  Year                     = {2003},
  Number                   = {5},
  Pages                    = {1782-1787},
  Volume                   = {19},

  Doi                      = {10.1021/la0261601},
  Owner                    = {paul},
  Timestamp                = {2012.02.14}
}

@Article{Lieto2004,
  Title                    = {Total Internal Reflection with Fluorescence Correlation Spectroscopy: Nonfluorescent Competitors},
  Author                   = {Alena M. Lieto and Nancy L. Thompson},
  Journal                  = {Biophysical Journal},
  Year                     = {2004},
  Number                   = {2},
  Pages                    = {1268 - 1278},
  Volume                   = {87},

  Doi                      = {10.1529/biophysj.103.035030},
  ISSN                     = {0006-3495},
  Owner                    = {paul},
  Timestamp                = {2012.02.14}
}

@Article{Muller2014,
  Title                    = {Scanning fluorescence correlation spectroscopy ({SFCS}) with a scan path perpendicular to the membrane plane},
  Author                   = {M\"{u}ller, P. and Schwille, P. and Weidemann, T.},
  Journal                  = {Methods Mol Biol},
  Year                     = {2014},
  Pages                    = {635--51},
  Volume                   = {1076},
  Abstract                 = {Scanning fluorescence correlation spectroscopy (SFCS) with a scan path perpendicular to the membrane plane was introduced to measure diffusion and interactions of fluorescent components in free-standing biomembranes. Using a confocal laser scanning microscope (CLSM), the open detection volume is repeatedly scanned through the membrane at a kHz frequency. The fluorescence photons emitted from the detection volume are continuously recorded and stored in a file. While the accessory hardware requirements for a conventional CLSM are minimal, data evaluation can pose a bottleneck. The photon events must be assigned to each scan, in which the maximum signal intensities have to be detected, binned, and aligned between the scans, in order to derive the membrane-related intensity fluctuations of one spot. Finally, this time-dependent signal must be correlated and evaluated by well-known FCS model functions. Here we provide two platform-independent, open source software tools (PyScanFCS and PyCorrFit) that allow to perform all of these steps and to establish perpendicular SFCS in its one- or two-focus as well as its single- or dual-color modality.},
  Doi                      = {10.1007/978-1-62703-649-8_29},
  Owner                    = {paul},
  Timestamp                = {2014.01.25}
}

@Article{Magde1972,
  Title                    = {Thermodynamic Fluctuations in a Reacting System - Measurement by Fluorescence Correlation Spectroscopy},
  Author                   = {Magde, Douglas and Elson, Elliot and Webb, W. W.},
  Journal                  = {Physical Review Letters},
  Year                     = {1972},

  Month                    = {Sep},
  Pages                    = {705--708},
  Volume                   = {29},

  Doi                      = {10.1103/PhysRevLett.29.705},
  Issue                    = {11},
  Owner                    = {paul},
  Publisher                = {American Physical Society},
  Timestamp                = {2012.11.01}
}

@Article{Magde1974,
  Title                    = {Fluorescence correlation spectroscopy. II. An experimental realization},
  Author                   = {Magde, Douglas and Elson, Elliot L. and Webb, Watt W.},
  Journal                  = {Biopolymers},
  Year                     = {1974},
  Number                   = {1},
  Pages                    = {29--61},
  Volume                   = {13},

  Doi                      = {10.1002/bip.1974.360130103},
  ISSN                     = {1097-0282},
  Owner                    = {paul},
  Publisher                = {Wiley Subscription Services, Inc., A Wiley Company},
  Timestamp                = {2012.09.21}
}

@Article{Magde1978,
  Title                    = {Fluorescence correlation spectroscopy. III. Uniform translation and laminar flow},
  Author                   = {Magde, D. and Webb, W. W. and Elson, E. L.},
  Journal                  = {Biopolymers},
  Year                     = {1978},
  Pages                    = {361--376},
  Volume                   = {17},

  Doi                      = {10.1002/bip.1978.360170208},
  Keywords                 = {FCS; laminar flow; capillary electrophoresis},
  Owner                    = {paul},
  Timestamp                = {2014.01.15}
}

@Article{Meseth1999,
  Title                    = {Resolution of fluorescence correlation measurements},
  Author                   = {Meseth, U. and Wohland, T. and Rigler, R. and Vogel, H.},
  Journal                  = {Biophys J},
  Year                     = {1999},
  Pages                    = {1619--1631},
  Volume                   = {76},

  Abstract                 = {The resolution limit of fluorescence correlation spectroscopy for two-component solutions is investigated theoretically and experimentally. The autocorrelation function for two different particles in solution were computed, statistical noise was added, and the resulting curve was fitted with a least squares fit. These simulations show that the ability to distinguish between two different molecular species in solution depends strongly on the number of photons detected from each particle, their difference in size, and the concentration of each component in solution. To distinguish two components, their diffusion times must differ by at least a factor of 1.6 for comparable quantum yields and a high fluorescence signal. Experiments were conducted with Rhodamine 6G and Rhodamine-labeled bovine serum albumin. The experimental results support the simulations. In addition, they show that even with a high fluorescence signal but significantly different quantum yields, the diffusion times must differ by a factor much bigger than 1.6 to distinguish the two components. Depending on the quantum yields and the difference in size, there exists a concentration threshold for the less abundant component below which it is not possible to determine with statistical means alone that two particles are in solution.},
  Doi                      = {10.1016/S0006-3495(99)77321-2},
  Keywords                 = {Diffusion, Multiple components},
  Owner                    = {TW},
  Timestamp                = {2014.01.27}
}

@Article{Nelder1965,
  Title                    = {A simplex method for function minimization},
  Author                   = {Nelder, John A and Mead, Roger},
  Journal                  = {Computer journal},
  Year                     = {1965},
  Number                   = {4},
  Pages                    = {308--313},
  Volume                   = {7},
  Doi                      = {10.1093/comjnl/7.4.308},
  Owner                    = {paul},
  Timestamp                = {2014.03.31}
}

@Article{Nitsche2004,
  Title                    = {A Transient Diffusion Model Yields Unitary Gap Junctional Permeabilities from Images of Cell-to-Cell Fluorescent Dye Transfer Between Xenopus Oocytes},
  Author                   = {Johannes M. Nitsche and Hou-Chien Chang and Paul A. Weber and Bruce J. Nicholson},
  Journal                  = {Biophysical Journal},
  Year                     = {2004},
  Number                   = {4},
  Pages                    = {2058 - 2077},
  Volume                   = {86},

  Doi                      = {10.1016/S0006-3495(04)74267-8},
  ISSN                     = {0006-3495},
  Owner                    = {paul},
  Timestamp                = {2012.11.08}
}

@Article{Ohsugi2009,
  Title                    = {Multipoint fluorescence correlation spectroscopy with total internal reflection fluorescence microscope},
  Author                   = {Ohsugi, Yu and Kinjo, Masataka},
  Journal                  = {Journal of Biomedical Optics},
  Year                     = {2009},
  Number                   = {1},
  Pages                    = {014030-014030-4},
  Volume                   = {14},

  Doi                      = {10.1117/1.3080723},
  Owner                    = {paul},
  Timestamp                = {2012.11.12}
}

@Article{Ohsugi2006,
  Title                    = {Lateral mobility of membrane-binding proteins in living cells measured by total internal reflection fluorescence correlation spectroscopy.},
  Author                   = {Ohsugi, Yu and Saito, Kenta and Tamura, Mamoru and Kinjo, Masataka},
  Journal                  = {Biophysical Journal},
  Year                     = {2006},
  Number                   = {9},
  Pages                    = {3456--3464},
  Volume                   = {91},

  Doi                      = {10.1529/biophysj.105.074625},
  Owner                    = {paul},
  Publisher                = {Biophysical Society},
  Timestamp                = {2012.02.14}
}

@Article{Palmer1987,
  Title                    = {Theory of sample translation in fluorescence correlation spectroscopy.},
  Author                   = {A. G. Palmer and N. L. Thompson},
  Journal                  = {Biophysical Journal},
  Year                     = {1987},

  Month                    = {Feb},
  Number                   = {2},
  Pages                    = {339--343},
  Volume                   = {51},

  Abstract                 = {New applications of the technique of fluorescence correlation spectroscopy (FCS) require lateral translation of the sample through a focused laser beam (Peterson, N.O., D.C. Johnson, and M.J. Schlesinger, 1986, Biophys. J., 49:817-820). Here, the effect of sample translation on the shape of the FCS autocorrelation function is examined in general. It is found that if the lateral diffusion coefficients of the fluorescent species obey certain conditions, then the FCS autocorrelation function is a simple product of one function that depends only on transport coefficients and another function that depends only on the rate constants of chemical reactions that occur in the sample. This simple form should allow manageable data analyses in new FCS experiments that involve sample translation.},
  Doi                      = {10.1016/S0006-3495(87)83340-4},
  Keywords                 = {Kinetics; Lasers; Mathematics; Models, Theoretical; Spectrometry, Fluorescence, methods},
  Language                 = {eng},
  Medline-pst              = {ppublish},
  Owner                    = {paul},
  Pii                      = {S0006-3495(87)83340-4},
  Pmid                     = {3828464},
  Timestamp                = {2012.11.02}
}

@Article{Pero2006-06,
  Title                    = {Size dependence of protein diffusion very close to membrane surfaces: measurement by total internal reflection with fluorescence correlation spectroscopy.},
  Author                   = {Pero, JK and Haas, EM and Thompson, NL},
  Journal                  = {The Journal of Physical Chemistry. B},
  Year                     = {2006},
  Number                   = {5},
  Pages                    = {10910-8},
  Volume                   = {110},

  Doi                      = {10.1021/jp056990y},
  ISSN                     = {1520-6106},
  Owner                    = {paul},
  Timestamp                = {2012.09.21}
}

@Article{Petrasek2010,
  Title                    = {Scanning {FCS} for the characterization of protein dynamics in live cells},
  Author                   = {Petr\'{a}\v{s}ek, Zden\v{e}k and Ries, J. and Schwille, P.},
  Journal                  = {Methods Enzymol},
  Year                     = {2010},
  Pages                    = {317--43},
  Volume                   = {472},

  Abstract                 = {Scanning fluorescence correlation spectroscopy (sFCS) is the generic term for a group of fluorescence correlation techniques where the measurement volume is moved across the sample in a defined way. The introduction of scanning is motivated by its ability to alleviate or remove several distinct problems often encountered in standard FCS, and thus, to extend the range of applicability of fluorescence correlation methods in biological systems. These problems include poor statistical accuracy in measurements with slowly moving molecules, photobleaching, optical distortions affecting the calibration of the measurement volume, membrane instabilities, etc. Here, we present an overview of sFCS methods, explaining their benefits, implementation details, requirements, and limitations, as well as relations to each other. Further, we give examples of different sFCS implementations as applied to cellular systems, namely large-circle sFCS to measure protein dynamics in embryo cortex and line sFCS to measure protein diffusion and interactions in unstable membranes.},
  Doi                      = {10.1016/s0076-6879(10)72005-x},
  Owner                    = {paul},
  Timestamp                = {2014.01.15}
}

@Article{Petrasek2008,
  Title                    = {Precise Measurement of Diffusion Coefficients using Scanning Fluorescence Correlation Spectroscopy},
  Author                   = {Petr\'{a}\v{s}ek, Zden\v{e}k and Schwille, Petra},
  Journal                  = {Biophysical Journal},
  Year                     = {2008},

  Month                    = feb,
  Number                   = {4},
  Pages                    = {1437--1448},
  Volume                   = {94},

  Doi                      = {10.1529/biophysj.107.108811},
  ISSN                     = {0006-3495},
  Owner                    = {paul},
  Publisher                = {Cell Press},
  Refid                    = {S0006-3495(08)70660-X DOI - 10.1529/biophysj.107.108811},
  Timestamp                = {2012.05.20}
}

@InCollection{Petrov:2008,
  Title                    = {State of the Art and Novel Trends in Fluorescence Correlation Spectroscopy},
  Author                   = {Petrov, E. P. and Schwille, P.},
  Booktitle                = {Standardization and Quality Assurance in Fluorescence Measurements II},
  Publisher                = {Springer Berlin Heidelberg},
  Year                     = {2008},
  Editor                   = {Resch-Genger, Ute},
  Pages                    = {145-197},
  Series                   = {Springer Series on Fluorescence},
  Volume                   = {6},

  Affiliation              = {Biophysics, BIOTEC, Technische Universität Dresden, Tatzberg 47–51, 01307 Dresden, Germany},
  Doi                      = {10.1007/4243_2008_032},
  ISBN                     = {978-3-540-70571-0},
  Keyword                  = {Chemistry}
}

@Article{Powell1964,
  Title                    = {An efficient method for finding the minimum of a function of several variables without calculating derivatives},
  Author                   = {Powell, M. J. D.},
  Journal                  = {The Computer Journal},
  Year                     = {1964},

  Month                    = {Feb},
  Number                   = {2},
  Pages                    = {155–162},
  Volume                   = {7},
  Doi                      = {10.1093/comjnl/7.2.155},
  ISSN                     = {1460-2067},
  Owner                    = {paul},
  Publisher                = {Oxford University Press (OUP)},
  Timestamp                = {2014.03.31}
}

@Article{Press,
  Title                    = {Numerical recipes},
  Author                   = {Press, William and Flannery, Brian P and Teukolsky, SAUL and Vetterling, WT},
  Journal                  = {Cambridge University Press},
  Year                     = {2006},
  Pages                    = {989},
  Volume                   = {1},

  __markedentry            = {[paul:]},
  Owner                    = {paul},
  Publisher                = {Cambridge Univ Press},
  Timestamp                = {2014.03.31}
}

@Article{Qian1991,
  Title                    = {Analysis of confocal laser-microscope optics for 3-D fluorescence correlation spectroscopy},
  Author                   = {Hong Qian and Elliot L. Elson},
  Journal                  = {Applied Optics},
  Year                     = {1991},

  Month                    = {Apr},
  Number                   = {10},
  Pages                    = {1185--1195},
  Volume                   = {30},

  Abstract                 = {Quantitative fluorescence correlation spectroscopy (FCS) and fluorescence photobleaching recovery (FPR) measurements in bulk solution require a well characterized confocal laser microscope optical system. The introduction of a characteristic function, the collection efficiency function (CEF), provides a quantitative theoretical analysis of this system, which yields an interpretation of the FCS and FPR measurements in three dimensions. We demonstrate that when the proper field diaphragm is introduced, the 3-D FCS measurements can be mimicked by a 2-D theory with only minor error. The FPR characteristic recovery time for diffusion is expected to be slightly longer than the corresponding time measured by FCS in the same conditions. This is because the profile of the laser beam used for photobleaching is not affected by the field diaphragm. The CEF is also important for quantitative analysis of standard scanning confocal microscopy when it is carried out using a finite detection pinhole.},
  Doi                      = {10.1364/AO.30.001185},
  Owner                    = {paul},
  Publisher                = {OSA},
  Timestamp                = {2012.11.02}
}

@Article{Richter2006,
  Title                    = {Formation of Solid-Supported Lipid Bilayers:  An Integrated View},
  Author                   = {Richter, Ralf P. and Bérat, Rémi and Brisson, Alain R.},
  Journal                  = {Langmuir},
  Year                     = {2006},
  Number                   = {8},
  Pages                    = {3497-3505},
  Volume                   = {22},

  Doi                      = {10.1021/la052687c},
  Owner                    = {paul},
  Timestamp                = {2012.11.12}
}

@PhdThesis{Ries:08,
  Title                    = {Advanced Fluorescence Correlation Techniques to Study Membrane Dynamics},
  Author                   = {Ries, E.},
  School                   = {Biophysics, BIOTEC, Technische Universität Dresden, Tatzberg 47–51, 01307 Dresden, Germany},
  Year                     = {2008},
  Note                     = {\url{http://nbn-resolving.de/urn:nbn:de:bsz:14-ds-1219846317196-73420}}
}

@Article{Ries2009,
  Title                    = {Accurate Determination of Membrane Dynamics with Line-Scan FCS},
  Author                   = {Jonas Ries and Salvatore Chiantia and Petra Schwille},
  Journal                  = {Biophysical Journal},
  Year                     = {2009},
  Number                   = {5},
  Pages                    = {1999 - 2008},
  Volume                   = {96},

  Doi                      = {10.1016/j.bpj.2008.12.3888},
  ISSN                     = {0006-3495},
  Owner                    = {paul},
  Timestamp                = {2012.11.08}
}

@Article{Ries2010,
  Title                    = {A comprehensive framework for fluorescence cross-correlation spectroscopy},
  Author                   = {Ries, J. and Petr\'{a}\v{s}ek, Zden\v{e}k and Garcia-Saez, A. J. and Schwille, P.},
  Journal                  = {New Journal of Physics},
  Year                     = {2010},
  Number                   = {11},
  Pages                    = {113009},
  Volume                   = {12},

  Abstract                 = {Dual-colour fluorescence cross-correlation spectroscopy is a powerful method of studying binding between labelled biomolecules in vitro as well as in vivo. However, numerous artefacts and experimental complexities complicate quantitative measurements. Here, we show that a combination of dual-colour fluorescence correlation spectroscopy (FCS) with dual-focus FCS avoids artefacts due to chromatic aberrations or saturation and circumvents the calibration of the detection volumes. In addition, we present a comprehensive mathematical framework that allows us to accurately analyse correlation curves even in the presence of spectral cross-talk, incomplete or stochastic labelling, multiple binding sites, a fluorescent background and depletion due to photobleaching. We demonstrate the merits of this approach using dual-colour dual-focus scanning FCS, which allows binding measurements on membranes not affected by membrane movements.},
  Doi                      = {10.1088/1367-2630/12/11/113009},
  Keywords                 = {living cells membrane dynamics diffusion molecules accurate fret fcs},
  Owner                    = {paul},
  Timestamp                = {2014.01.15}
}

@Article{Ries2008390,
  Title                    = {Total Internal Reflection Fluorescence Correlation Spectroscopy: Effects of Lateral Diffusion and Surface-Generated Fluorescence},
  Author                   = {Jonas Ries and Eugene P. Petrov and Petra Schwille},
  Journal                  = {Biophysical Journal},
  Year                     = {2008},
  Number                   = {1},
  Pages                    = {390 - 399},
  Volume                   = {95},

  Doi                      = {10.1529/biophysj.107.126193},
  ISSN                     = {0006-3495}
}

@Article{Ries2008,
  Title                    = {New concepts for fluorescence correlation spectroscopy on membranes},
  Author                   = {Ries, Jonas and Schwille, Petra},
  Journal                  = {Physical Chemistry Chemical Physics},
  Year                     = {2008},
  Number                   = {24},
  Pages                    = {--},
  Volume                   = {10},

  Abstract                 = {Fluorescence correlation spectroscopy (FCS) is a powerful tool to measure useful physical quantities such as concentrations, diffusion coefficients, diffusion modes or binding parameters, both in model and cell membranes. However, it can suffer from severe artifacts, especially in non-ideal systems. Here we assess the potential and limitations of standard confocal FCS on lipid membranes and present recent developments which facilitate accurate and quantitative measurements on such systems. In particular, we discuss calibration-free diffusion and concentration measurements using z-scan FCS and two focus FCS and present several approaches using scanning FCS to accurately measure slow dynamics. We also show how surface confined FCS enables the study of membrane dynamics even in presence of a strong cytosolic background and how FCS with a variable detection area can reveal submicroscopic heterogeneities in cell membranes.},
  Doi                      = {10.1039/b718132a},
  ISSN                     = {1463-9076},
  Owner                    = {paul},
  Publisher                = {The Royal Society of Chemistry},
  Timestamp                = {2012.02.14}
}

@Article{Ries2006,
  Title                    = {Studying slow membrane dynamics with continuous wave scanning fluorescence correlation spectroscopy},
  Author                   = {Ries, J. and Schwille, P.},
  Journal                  = {Biophys J},
  Year                     = {2006},
  Number                   = {5},
  Pages                    = {1915--24},
  Volume                   = {91},
  Abstract                 = {Here we discuss the application of scanning fluorescence correlation spectroscopy (SFCS) using continuous wave excitation to analyze membrane dynamics. The high count rate per molecule enables the study of very slow diffusion in model and cell membranes, as well as the application of two-foci fluorescence cross-correlation spectroscopy for parameter-free determination of diffusion constants. The combination with dual-color fluorescence cross-correlation spectroscopy with continuous or pulsed interleaved excitation allows binding studies on membranes. Reduction of photobleaching, higher reproducibility, and stability compared to traditional FCS on membranes, and the simple implementation in a commercial microscopy setup make SFCS a valuable addition to the pool of fluorescence fluctuation techniques.},
  Doi                      = {10.1529/biophysj.106.082297},
  Keywords                 = {Biological Transport, Active/physiology Cell Membrane/*chemistry/*metabolism Diffusion Membrane Proteins/analysis/*chemistry/*metabolism Spectrometry, Fluorescence/*methods Time Factors},
  Owner                    = {paul},
  Timestamp                = {2014.01.25}
}

@Article{Rigler1993,
  Title                    = {Fluorescence correlation spectroscopy with high count rate and low background: analysis of translational diffusion},
  Author                   = {Rigler, R. and Mets, {\"U}. and Widengren, J. and Kask, P.},
  Journal                  = {European Biophysics Journal},
  Year                     = {1993},
  Pages                    = {169-175},
  Volume                   = {22},

  Doi                      = {10.1007/BF00185777},
  ISSN                     = {0175-7571},
  Issue                    = {3},
  Keywords                 = {Fluorescence correlation spectroscopy; Fluorescence intensity fluctuations; Translational diffusion; Epifluorescence microscope; Silicon photon counter},
  Language                 = {English},
  Owner                    = {paul},
  Publisher                = {Springer-Verlag},
  Timestamp                = {2012.11.02}
}

@Article{Rippe2000,
  Title                    = {Simultaneous binding of two {DNA} duplexes to the NtrC-enhancer complex studied by two-color fluorescence cross-correlation spectroscopy},
  Author                   = {Rippe, K.},
  Journal                  = {Biochemistry},
  Year                     = {2000},
  Number                   = {9},
  Pages                    = {2131--9},
  Volume                   = {39},

  Abstract                 = {The transcription activator protein NtrC (nitrogen regulatory protein C, also termed NR(I)) can catalyze the transition of Escherichia coli RNA polymerase complexed with the sigma(54) factor (RNAP x sigma(54)) from the closed complex (RNAP x sigma(54) bound at the promoter) to the open complex (melting of the promoter DNA). This process involves phosphorylation of NtrC (NtrC-P), assembly of an octameric NtrC-P complex at the enhancer DNA sequence, interaction of this complex with promoter-bound RNAP x sigma(54) via DNA looping, and hydrolysis of ATP. Here it is demonstrated by two-color fluorescence cross-correlation spectroscopy measurements of 6-carboxyfluorescein and 6-carboxy-X-rhodamine-labeled DNA oligonucleotide duplexes that the NtrC-P complex can bind two DNA duplexes simultaneously. This suggests a model for the conformation of the looped intermediate that is formed between NtrC-P and RNAP. sigma(54) at the glnAp2 promoter during the activation process.},
  Doi                      = {10.1021/bi9922190},
  Keywords                 = {Bacterial Proteins/chemistry/*metabolism Base Sequence DNA, Bacterial/chemistry/*metabolism DNA-Binding Proteins/chemistry/*metabolism Diffusion *Enhancer Elements (Genetics) Escherichia coli/chemistry/genetics Escherichia coli Proteins Models, Chemical Models, Molecular Molecular Sequence Data Nucleic Acid Heteroduplexes/chemistry/*metabolism PII Nitrogen Regulatory Proteins Phosphorylation Protein Binding Reproducibility of Results Spectrometry, Fluorescence/methods *Trans-Activators *Transcription Factors},
  Owner                    = {paul},
  Timestamp                = {2014.01.15}
}

@Article{Ruan2004,
  Title                    = {Spatial-Temporal Studies of Membrane Dynamics: Scanning Fluorescence Correlation Spectroscopy (SFCS)},
  Author                   = {Ruan, Qiaoqiao and Cheng, Melanie A. and Levi, Moshe and Gratton, Enrico and Mantulin, William W.},
  Journal                  = {Biophysical Journal},
  Year                     = {2004},

  Month                    = aug,
  Number                   = {2},
  Pages                    = {1260--1267},
  Volume                   = {87},

  Doi                      = {10.1529/biophysj.103.036483},
  ISSN                     = {0006-3495},
  Owner                    = {paul},
  Publisher                = {Cell Press},
  Refid                    = {S0006-3495(04)73605-X DOI - 10.1529/biophysj.103.036483},
  Timestamp                = {2012.02.14}
}

@Article{Sankaran2009,
  Title                    = {Diffusion, Transport, and Cell Membrane Organization Investigated by Imaging Fluorescence Cross-Correlation Spectroscopy},
  Author                   = {Sankaran, Jagadish and Manna, Manoj and Guo, Lin and Kraut, Rachel and Wohland, Thorsten},
  Journal                  = {Biophysical Journal},
  Year                     = {2009},

  Month                    = nov,
  Number                   = {9},
  Pages                    = {2630--2639},
  Volume                   = {97},

  Doi                      = {10.1016/j.bpj.2009.08.025},
  ISSN                     = {0006-3495},
  Owner                    = {paul},
  Publisher                = {Cell Press},
  Refid                    = {S0006-3495(09)01387-3 DOI - 10.1016/j.bpj.2009.08.025},
  Timestamp                = {2012.09.21}
}

@Article{Sankaran2010,
  Title                    = {ImFCS: a software for imaging FCS data analysis and visualization.},
  Author                   = {Jagadish Sankaran and Xianke Shi and Liang Yoong Ho and Ernst H K Stelzer and Thorsten Wohland},
  Journal                  = {Optics Express},
  Year                     = {2010},

  Month                    = {Dec},
  Number                   = {25},
  Pages                    = {25468--25481},
  Volume                   = {18},

  Abstract                 = {The multiplexing of fluorescence correlation spectroscopy (FCS), especially in imaging FCS using fast, sensitive array detectors, requires the handling of large amounts of data. One can easily collect in excess of 100,000 FCS curves a day, too many to be treated manually. Therefore, ImFCS, an open-source software which relies on standard image files was developed and provides a wide range of options for the calculation of spatial and temporal auto- and cross-correlations, as well as differences in Cross-Correlation Functions (ΔCCF). ImFCS permits fitting of standard models to correlation functions and provides optimized histograms of fitted parameters. Applications include the measurement of diffusion and flow with Imaging Total Internal Reflection FCS (ITIR-FCS) and Single Plane Illumination Microscopy FCS (SPIM-FCS) in biologically relevant samples. As a compromise between ITIR-FCS and SPIM-FCS, we extend the applications to Imaging Variable Angle-FCS (IVA-FCS) where sub-critical oblique illumination provides sample sectioning close to the cover slide.},
  Doi                      = {10.1364/OE.18.025468},
  Institution              = {Singapore-MIT Alliance, National University of Singapore, E4-04-10, 4 Engineering Drive 3, 117576 Singapore.},
  Keywords                 = {Algorithms; Pattern Recognition, Automated, methods; Software; Spectrometry, Fluorescence, methods},
  Language                 = {eng},
  Medline-pst              = {ppublish},
  Owner                    = {paul},
  Pii                      = {208325},
  Pmid                     = {21164894},
  Timestamp                = {2012.10.24}
}

@Article{SbalzariniSPT,
  Title                    = {Feature Point Tracking and Trajectory Analysis for Video Imaging in Cell Biology},
  Author                   = {I. F. Sbalzarini and P. Koumoutsakos},
  Journal                  = {Journal of Structural Biology},
  Year                     = {2005},
  Pages                    = {182-195},
  Volume                   = {151(2)},

  Doi                      = {10.1016/j.jsb.2005.06.002},
  Owner                    = {paul},
  Timestamp                = {2012.10.16}
}

@Article{Schatzel1990,
  Title                    = {Noise on photon correlation data. I. Autocorrelation functions},
  Author                   = {K. Sch{\"a}tzel},
  Journal                  = {Quantum Optics: Journal of the European Optical Society Part B},
  Year                     = {1990},
  Number                   = {4},
  Pages                    = {287},
  Volume                   = {2},

  Abstract                 = {An adequate analysis of photon correlation data requires knowledge about the statistical accuracy of the measured data. For the model of gamma-distributed intensities, that is including the effect of a finite intercept, the full covariance matrix is calculated for all the channels of the photon autocorrelation functions. A thorough discussion of multiple sample time correlation illuminates the importance of temporal averaging effects at large lag times. A practical estimation scheme is given for the noise in photon correlation data from a multiple sample time measurement.},
  Doi                      = {10.1088/0954-8998/2/4/002},
  Owner                    = {paul},
  Timestamp                = {2012.11.02}
}

@Article{Schwille1999,
  Title                    = {Molecular dynamics in living cells observed by fluorescence correlation spectroscopy with one- and two-photon excitation},
  Author                   = {Schwille, P. and Haupts, U. and Maiti, S. and Webb, W. W.},
  Journal                  = {Biophys J},
  Year                     = {1999},
  Number                   = {4},
  Pages                    = {2251--65},
  Volume                   = {77},

  Abstract                 = {Multiphoton excitation (MPE) of fluorescent probes has become an attractive alternative in biological applications of laser scanning microscopy because many problems encountered in spectroscopic measurements of living tissue such as light scattering, autofluorescence, and photodamage can be reduced. The present study investigates the characteristics of two-photon excitation (2PE) in comparison with confocal one-photon excitation (1PE) for intracellular applications of fluorescence correlation spectroscopy (FCS). FCS is an attractive method of measuring molecular concentrations, mobility parameters, chemical kinetics, and fluorescence photophysics. Several FCS applications in mammalian and plant cells are outlined, to illustrate the capabilities of both 1PE and 2PE. Photophysical properties of fluorophores required for quantitative FCS in tissues are analyzed. Measurements in live cells and on cell membranes are feasible with reasonable signal-to-noise ratios, even with fluorophore concentrations as low as the single-molecule level in the sampling volume. Molecular mobilities can be measured over a wide range of characteristic time constants from approximately 10(-3) to 10(3) ms. While both excitation alternatives work well for intracellular FCS in thin preparations, 2PE can substantially improve signal quality in turbid preparations like plant cells and deep cell layers in tissue. At comparable signal levels, 2PE minimizes photobleaching in spatially restrictive cellular compartments, thereby preserving long-term signal acquisition.},
  Doi                      = {10.1016/s0006-3495(99)77065-7},
  Keywords                 = {Animals Calibration Cell Line Cell Membrane/*metabolism/radiation effects Cell Wall/*metabolism/radiation effects Cytoplasm/*metabolism/radiation effects Diffusion Fluorescence Fluorescent Dyes/*metabolism Green Fluorescent Proteins Humans Kinetics Luminescent Proteins/metabolism Photochemistry *Photons Plant Leaves/cytology/radiation effects Plants, Toxic Rhodamines/metabolism Spectrometry, Fluorescence/instrumentation/*methods Tobacco},
  Owner                    = {paul},
  Timestamp                = {2014.01.15}
}

@Article{Schwille2000,
  Title                    = {Fluorescence correlation spectroscopy reveals fast optical excitation-driven intramolecular dynamics of yellow fluorescent proteins},
  Author                   = {Schwille, Petra and Kummer, Susanne and Heikal, Ahmed A. and Moerner, W. E. and Webb, Watt W.},
  Journal                  = {Proceedings of the National Academy of Sciences},
  Year                     = {2000},
  Number                   = {1},
  Pages                    = {151-156},
  Volume                   = {97},

  Abstract                 = {Fast excitation-driven fluctuations in the fluorescence emission of yellow-shifted green fluorescent protein mutants T203Y and T203F, with S65G/S72A, are discovered in the 10−6–10−3-s time range, by using fluorescence correlation spectroscopy at 10−8 M. This intensity-dependent flickering is conspicuous at high pH, with rate constants independent of pH and viscosity with a minor temperature effect. The mean flicker rate increases linearly with excitation intensity for at least three decades, but the mean dark fraction of the molecules undergoing these dynamics is independent of illumination intensity over ≈6 × 102 to 5 × 106 W/cm2. These results suggest that optical excitation establishes an equilibration between two molecular states of different spectroscopic properties that are coupled only via the excited state as a gateway. This reversible excitation-driven transition has a quantum efficiency of ≈10−3. Dynamics of external protonation, reversibly quenching the fluorescence, are also observed at low pH in the 10- to 100-μs time range. The independence of these two bright–dark flicker processes implies the existence of at least two separate dark states of these green fluorescent protein mutants. Time-resolved fluorescence measurements reveal a single exponential decay of the excited state population with 3.8-ns lifetime, after 500-nm excitation, that is pH independent. Our fluorescence correlation spectroscopy results are discussed in terms of recent theoretical studies that invoke isomerization of the chromophore as a nonradiative channel of the excited state relaxation.},
  Doi                      = {10.1073/pnas.97.1.151},
  Owner                    = {paul},
  Timestamp                = {2012.09.24}
}

@Article{Schwille1997,
  Title                    = {Dual-color fluorescence cross-correlation spectroscopy for multicomponent diffusional analysis in solution},
  Author                   = {Schwille, P. and Meyer-Almes, F.J. and Rigler, R.},
  Journal                  = {Biophysical Journal},
  Year                     = {1997},

  Month                    = apr,
  Number                   = {4},
  Pages                    = {1878--1886},
  Volume                   = {72},

  Doi                      = {10.1016/s0006-3495(97)78833-7},
  ISSN                     = {0006-3495},
  Owner                    = {paul},
  Publisher                = {Cell Press},
  Refid                    = {S0006-3495(97)78833-7 DOI - 10.1016/S0006-3495(97)78833-7},
  Timestamp                = {2012.02.14}
}

@Article{Scomparin2009,
  Title                    = {Diffusion in supported lipid bilayers: Influence of substrate and preparation technique on the internal dynamics},
  Author                   = {Scomparin, C. and Lecuyer, S. and Ferreira, M. and Charitat, T. and Tinland, B.},
  Journal                  = {The European Physical Journal E: Soft Matter and Biological Physics},
  Year                     = {2009},
  Pages                    = {211-220},
  Volume                   = {28},

  Affiliation              = {CNRS UPR 3118 CINAM 13288 Marseille Cedex 09 France},
  Doi                      = {10.1140/epje/i2008-10407-3},
  ISSN                     = {1292-8941},
  Issue                    = {2},
  Keyword                  = {Physik und Astronomie},
  Owner                    = {paul},
  Publisher                = {Springer Berlin / Heidelberg},
  Timestamp                = {2012.10.22}
}

@Article{Seu2007,
  Title                    = {Effect of Surface Treatment on Diffusion and Domain Formation in Supported Lipid Bilayers},
  Author                   = {Seu, Kalani J. and Pandey, Anjan P. and Haque, Farzin and Proctor, Elizabeth A. and Ribbe, Alexander E. and Hovis, Jennifer S.},
  Journal                  = {Biophysical Journal},
  Year                     = {2007},

  Month                    = apr,
  Number                   = {7},
  Pages                    = {2445--2450},
  Volume                   = {92},

  Doi                      = {10.1529/biophysj.106.099721},
  ISSN                     = {0006-3495},
  Owner                    = {paul},
  Publisher                = {Cell Press},
  Refid                    = {S0006-3495(07)71049-4 DOI - 10.1529/biophysj.106.099721},
  Timestamp                = {2012.10.22}
}

@Article{Shannon1984,
  Title                    = {Communication in the presence of noise},
  Author                   = {Shannon, C.E.},
  Journal                  = {Proceedings of the IEEE},
  Year                     = {1984},

  Month                    = {sept.},
  Number                   = {9},
  Pages                    = { 1192 - 1201},
  Volume                   = {72},

  Doi                      = {10.1109/PROC.1984.12998},
  ISSN                     = {0018-9219},
  Owner                    = {paul},
  Timestamp                = {2012.11.12}
}

@Article{Skinner2005,
  Title                    = {Position-sensitive scanning fluorescence correlation spectroscopy.},
  Author                   = {Joseph P Skinner and Yan Chen and Joachim D Müller},
  Journal                  = {Biophysical Journal},
  Year                     = {2005},

  Month                    = {Aug},
  Number                   = {2},
  Pages                    = {1288--1301},
  Volume                   = {89},

  Abstract                 = {Fluorescence correlation spectroscopy (FCS) uses a stationary laser beam to illuminate a small sample volume and analyze the temporal behavior of the fluorescence fluctuations within the stationary observation volume. In contrast, scanning FCS (SFCS) collects the fluorescence signal from a moving observation volume by scanning the laser beam. The fluctuations now contain both temporal and spatial information about the sample. To access the spatial information we synchronize scanning and data acquisition. Synchronization allows us to evaluate correlations for every position along the scanned trajectory. We use a circular scan trajectory in this study. Because the scan radius is constant, the phase angle is sufficient to characterize the position of the beam. We introduce position-sensitive SFCS (PSFCS), where correlations are calculated as a function of lag time and phase. We present the theory of PSFCS and derive expressions for diffusion, diffusion in the presence of flow, and for immobilization. To test PSFCS we compare experimental data with theory. We determine the direction and speed of a flowing dye solution and the position of an immobilized particle. To demonstrate the feasibility of the technique for applications in living cells we present data of enhanced green fluorescent protein measured in the nucleus of COS cells.},
  Doi                      = {10.1529/biophysj.105.060749},
  Institution              = {School of Physics and Astronomy, University of Minnesota, Minneapolis, 55455, USA. josephs@physics.umn.edu},
  Keywords                 = {Algorithms; Image Enhancement, methods; Image Interpretation, Computer-Assisted, methods; Information Storage and Retrieval, methods; Microscopy, Confocal, methods; Reproducibility of Results; Sensitivity and Specificity; Spectrometry, Fluorescence, methods},
  Language                 = {eng},
  Medline-pst              = {ppublish},
  Owner                    = {paul},
  Pii                      = {S0006-3495(05)72776-4},
  Pmid                     = {15894645},
  Timestamp                = {2012.10.28}
}

@Article{Starr2001,
  Title                    = {Total Internal Reflection with Fluorescence Correlation Spectroscopy: Combined Surface Reaction and Solution Diffusion},
  Author                   = {Tammy E. Starr and Nancy L. Thompson},
  Journal                  = {Biophysical Journal},
  Year                     = {2001},
  Number                   = {3},
  Pages                    = {1575 - 1584},
  Volume                   = {80},

  Doi                      = {10.1016/S0006-3495(01)76130-9},
  ISSN                     = {0006-3495}
}

@Article{Sutherland1905,
  Title                    = {A dynamical theory of diffusion for non-electrolytes and the molecular mass of albumin},
  Author                   = {Sutherland, William},
  Journal                  = {Philosophical Magazine Series 6},
  Year                     = {1905},
  Number                   = {54},
  Pages                    = {781-785},
  Volume                   = {9},

  __markedentry            = {[paul]},
  Doi                      = {10.1080/14786440509463331},
  Owner                    = {paul},
  Timestamp                = {2012.11.14}
}

@Article{Tamm1985,
  Title                    = {Supported phospholipid bilayers},
  Author                   = {Tamm, L.K. and McConnell, H.M.},
  Journal                  = {Biophysical Journal},
  Year                     = {1985},

  Month                    = jan,
  Number                   = {1},
  Pages                    = {105--113},
  Volume                   = {47},

  Doi                      = {10.1016/S0006-3495(85)83882-0},
  ISSN                     = {0006-3495},
  Owner                    = {paul},
  Publisher                = {Cell Press},
  Refid                    = {S0006-3495(85)83882-0 DOI - 10.1016/S0006-3495(85)83882-0},
  Timestamp                = {2012.10.29}
}

@InCollection{Thomps:bookFCS2002,
  Title                    = {Fluorescence Correlation Spectroscopy},
  Author                   = {Thompson, Nancy},
  Booktitle                = {Topics in Fluorescence Spectroscopy},
  Publisher                = {Springer US},
  Year                     = {2002},
  Editor                   = {Lakowicz, Joseph and Geddes, Chris D. and Lakowicz, Joseph R.},
  Pages                    = {337-378},
  Series                   = {Topics in Fluorescence Spectroscopy},
  Volume                   = {1},

  Affiliation              = {University of North Carolina at Chapel Hill Department of Chemistry Chapel Hill North Carolina 27599-3290 USA},
  Doi                      = {10.1007/0-306-47057-8_6},
  ISBN                     = {978-0-306-47057-8},
  Keyword                  = {Biomedical and Life Sciences},
  Owner                    = {paul},
  Timestamp                = {2012.01.10}
}

@InBook{Thompson1991,
  Title                    = {Fluorescence Correlation Spectroscopy},
  Author                   = {Thompson, N.L.},
  Editor                   = {Lankowicz, J.R.},
  Pages                    = {337--378},
  Publisher                = {Plenum Press},
  Year                     = {1991},

  Address                  = {New York},
  Edition                  = {Techniques},
  Series                   = {Topics in Fluorescence Spectroscopy},
  Volume                   = {1},

  Booktitle                = {Topics in Fluorescence Spectroscopy},
  Owner                    = {paul},
  Timestamp                = {2014.01.15}
}

@Article{Thompson1983,
  Title                    = {Immunoglobulin surface-binding kinetics studied by total internal reflection with fluorescence correlation spectroscopy},
  Author                   = {N.L. Thompson and D. Axelrod},
  Journal                  = {Biophysical Journal},
  Year                     = {1983},
  Number                   = {1},
  Pages                    = {103 - 114},
  Volume                   = {43},

  Doi                      = {10.1016/S0006-3495(83)84328-8},
  ISSN                     = {0006-3495},
  Owner                    = {paul},
  Timestamp                = {2012.02.14}
}

@Article{Thompson1981,
  Title                    = {Measuring surface dynamics of biomolecules by total internal reflection fluorescence with photobleaching recovery or correlation spectroscopy},
  Author                   = {N.L. Thompson and T.P. Burghardt and D. Axelrod},
  Journal                  = {Biophysical Journal},
  Year                     = {1981},
  Number                   = {3},
  Pages                    = {435 - 454},
  Volume                   = {33},

  Doi                      = {10.1016/S0006-3495(81)84905-3},
  ISSN                     = {0006-3495},
  Owner                    = {paul},
  Timestamp                = {2012.02.14}
}

@Article{Thompson1997,
  Title                    = {Equilibrium, Kinetics, Diffusion and Self-Association of Proteins at Membrane Surfaces: Measurement by Total Internal Reflection Fluorescence Microscopy},
  Author                   = {Thompson, Nancy L. and Drake, Andrew W. and Chen, Lixin and Broek, Willem Vanden},
  Journal                  = {Photochemistry and Photobiology},
  Year                     = {1997},
  Number                   = {1},
  Pages                    = {39--46},
  Volume                   = {65},

  Doi                      = {10.1111/j.1751-1097.1997.tb01875.x},
  ISSN                     = {1751-1097},
  Owner                    = {paul},
  Publisher                = {Blackwell Publishing Ltd},
  Timestamp                = {2012.02.14}
}

@Article{Thompson1997a,
  Title                    = {Total internal reflection fluorescence: applications in cellular biophysics},
  Author                   = {Nancy L Thompson and B Christoffer Lagerholm},
  Journal                  = {Current Opinion in Biotechnology},
  Year                     = {1997},
  Number                   = {1},
  Pages                    = {58 - 64},
  Volume                   = {8},

  Doi                      = {10.1016/S0958-1669(97)80158-9},
  ISSN                     = {0958-1669},
  Owner                    = {paul},
  Timestamp                = {2012.02.14}
}

@Article{Thompson2007,
  Title                    = {Total internal reflection with fluorescence correlation spectroscopy},
  Author                   = {Thompson, N. L. and Steele, B. L.},
  Journal                  = {Nat Protoc},
  Year                     = {2007},
  Number                   = {4},
  Pages                    = {878--90},
  Volume                   = {2},
  Abstract                 = {Total internal reflection-fluorescence correlation spectroscopy (TIR-FCS) is an emerging technique that is used to measure events at or near an interface, including local fluorophore concentrations, local translational mobilities and the kinetic rate constants that describe the association and dissociation of fluorophores at the interface. TIR-FCS is also an extremely promising method for studying dynamics at or near the basal membranes of living cells. This protocol gives a general overview of the steps necessary to construct and test a TIR-FCS system using either through-prism or through-objective internal reflection geometry adapted for FCS. The expected forms of the autocorrelation function are discussed for the cases in which fluorescent molecules in solution diffuse through the depth of the evanescent field, but do not bind to the surface of interest, and in which reversible binding to the surface also occurs.},
  Doi                      = {10.1038/nprot.2007.110},
  Keywords                 = {Fluorescent Dyes/analysis Kinetics Ligands Spectrometry, Fluorescence/instrumentation/*methods},
  Owner                    = {paul},
  Timestamp                = {2014.01.25}
}

@Article{Toomre2001,
  Title                    = {Lighting up the cell surface with evanescent wave microscopy},
  Author                   = {Derek Toomre and Dietmar J. Manstein},
  Journal                  = {Trends in Cell Biology},
  Year                     = {2001},
  Number                   = {7},
  Pages                    = {298 - 303},
  Volume                   = {11},

  Doi                      = {10.1016/S0962-8924(01)02027-X},
  ISSN                     = {0962-8924},
  Keywords                 = {green-fluorescent protein (GFP)},
  Owner                    = {paul},
  Timestamp                = {2012.02.14}
}

@Article{Unruh2008,
  Title                    = {Analysis of Molecular Concentration and Brightness from Fluorescence Fluctuation Data with an Electron Multiplied CCD Camera},
  Author                   = {Unruh, Jay R. and Gratton, Enrico},
  Journal                  = {Biophysical Journal},
  Year                     = {2008},

  Month                    = dec,
  Number                   = {11},
  Pages                    = {5385--5398},
  Volume                   = {95},

  Doi                      = {10.1529/biophysj.108.130310},
  ISSN                     = {0006-3495},
  Owner                    = {paul},
  Publisher                = {Cell Press},
  Refid                    = {S0006-3495(08)78962-8 DOI - 10.1529/biophysj.108.130310},
  Timestamp                = {2012.09.21}
}

@Article{Vacha2009,
  Title                    = {Effects of Alkali Cations and Halide Anions on the DOPC Lipid Membrane},
  Author                   = {V\'{a}cha, Robert and Siu, Shirley W. I. and Petrov, Michal and Böckmann, Rainer A. and Barucha-Kraszewska, Justyna and Jurkiewicz, Piotr and Hof, Martin and Berkowitz, Max L. and Jungwirth, Pavel},
  Journal                  = {The Journal of Physical Chemistry A},
  Year                     = {2009},
  Number                   = {26},
  Pages                    = {7235-7243},
  Volume                   = {113},

  Doi                      = {10.1021/jp809974e},
  Owner                    = {paul},
  Timestamp                = {2012.10.24}
}

@Article{Wachsmuth2000,
  Title                    = {Anomalous diffusion of fluorescent probes inside living cell nuclei investigated by spatially-resolved fluorescence correlation spectroscopy},
  Author                   = {Wachsmuth, M. and Waldeck, W. and Langowski, J.},
  Journal                  = {J Mol Biol},
  Year                     = {2000},
  Number                   = {4},
  Pages                    = {677--89},
  Volume                   = {298},

  Abstract                 = {We have investigated spatial variations of the diffusion behavior of the green fluorescent protein mutant EGFP (F64L/S65T) and of the EGFP-beta-galactosidase fusion protein in living cells with fluorescence correlation spectroscopy. Our fluorescence correlation spectroscopy device, in connection with a precision x-y translation stage, provides submicron spatial resolution and a detection volume smaller than a femtoliter. The fluorescence fluctuations in cell lines expressing EGFP are caused by molecular diffusion as well as a possible internal and a pH-dependent external protonation process of the EGFP chromophore. The latter processes result in two apparent nonfluorescent states that have to be taken into account when evaluating the fluorescence correlation spectroscopy data. The diffusional contribution deviates from ideal behavior and depends on the position in the cell. The fluorescence correlation spectroscopy data can either be evaluated as a two component model with one fraction of the molecules undergoing free Brownian motion with a diffusion coefficient approximately five times smaller than in aqueous solution, and another fraction diffusing one or two orders of magnitude slower. This latter component is especially noticeable in the nuclei. Alternatively, we can fit the data to an anomalous diffusion model where the time dependence of the diffusion serves as a measure for the degree of obstruction, which is large especially in nuclei. Possible mechanisms for this long tail behavior include corralling, immobile obstacles, and binding with a broad distribution of binding affinities. The results are consistent with recent numerical models of the chromosome territory structure in the cell nucleus.},
  Doi                      = {10.1006/jmbi.2000.3692},
  Keywords                 = {Animals COS Cells Cell Line Cell Nucleus/chemistry/*metabolism Cell Survival Cytoplasm/chemistry/metabolism Diffusion Fluorescence Fluorescent Dyes/*metabolism Genetic Vectors/genetics Green Fluorescent Proteins Hydrogen-Ion Concentration Kinetics Luminescent Proteins/chemistry/genetics/metabolism Models, Biological Protein Conformation Protons Recombinant Fusion Proteins/chemistry/genetics/metabolism Solutions Spectrometry, Fluorescence Statistics Transfection},
  Owner                    = {paul},
  Timestamp                = {2014.01.15}
}

@Article{Weidemann2013,
  Title                    = {Dual-color fluorescence cross-correlation spectroscopy with continuous laser excitation in a confocal setup},
  Author                   = {Weidemann, T. and Schwille, P.},
  Journal                  = {Methods Enzymol},
  Year                     = {2013},
  Pages                    = {43--70},
  Volume                   = {518},

  Abstract                 = {Fluorescence correlation spectroscopy evaluates local signal fluctuations arising from stochastic movements of fluorescent particles in solution. The measured fluctuating signal is correlated in time and analyzed with appropriate model functions containing the parameters that describe the underlying molecular behavior. The dual-color extension, fluorescence cross-correlation spectroscopy (FCCS) allows for a comparison between spectrally well-separated channels to extract codiffusion events that reflect interactions between differently labeled molecules. In addition to solution measurements, FCCS can be applied with subcellular resolution and is therefore a very promising approach for a quantitative biochemical assessment of molecular networks in living cells. To derive thermodynamic and kinetic reaction parameters, the influence of a number of other factors like background noise, illumination intensity profiles, photophysical processes, and cross talk between the channels have to be treated. Here, we provide a roadmap to derive binding reaction data with dual-color FCCS using continuous wave laser excitation, as it is now accessible with many state-of-the-art confocal microscopes.},
  Doi                      = {10.1016/B978-0-12-388422-0.00003-0},
  Owner                    = {paul},
  Timestamp                = {2014.01.15}
}

@Book{Weidemann2009,
  Title                    = {Fluorescence Correlation Spectroscopy in Living Cells},
  Author                   = {Weidemann, T. and Schwille, P.},
  Publisher                = {Springer},
  Year                     = {2009},

  Address                  = {Heidelberg},
  Series                   = {Handbook of Single-Molecule Biophysics},

  Owner                    = {paul},
  Pages                    = {648},
  Timestamp                = {2014.01.15}
}

@Article{Weidemann2002,
  Title                    = {Analysis of Ligand Binding by Two-Colour Fluorescence Cross-Correlation Spectroscopy},
  Author                   = {Weidemann, T. and Wachsmuth, M. and Tewes, M and Rippe, K. and Langowski, J.},
  Journal                  = {Single Mol},
  Year                     = {2002},
  Number                   = {1},
  Pages                    = {49--61},
  Volume                   = {3},

  Abstract                 = {Fluorescence correlation spectroscopy (FCS) is a well-established method for the analysis of freely diffusing fluorescent particles in solution. In a two-colour setup, simultaneous detection of two different dyes allows the acquisition of both the autocorrelation of the signal of each channel and the cross-correlation of the two channels (fluorescence cross correlation spectroscopy, FCCS). The cross-correlation function is related to the amount of diffusing particles carrying both dyes and can be used for monitoring a binding reaction. Here we develop a formalism for a quantitative analysis of ligand binding from a combination of the auto- and the cross-correlation amplitudes. Technical constraints, like the focal geometry, background signal and cross-talk between the detection channels as well as photophysical and biochemical effects which modulate the brightness of the particles are included in the analysis. Based on this framework a comprehensive treatment for the determination of two-component binding equilibria by FCS/FCCS is presented.},
  Doi                      = {10.1002/1438-5171(200204)3:1<49::aid-simo49>3.0.co;2-t},
  Keywords                 = {FCS FCCS receptor-ligand binding protein-DNA interactions},
  Owner                    = {paul},
  Timestamp                = {2014.01.15}
}

@Article{Weiss2003,
  Title                    = {Anomalous protein diffusion in living cells as seen by fluorescence correlation spectroscopy},
  Author                   = {Weiss, M. and Hashimoto, H. and Nilsson, T.},
  Journal                  = {Biophys J},
  Year                     = {2003},
  Number                   = {6},
  Pages                    = {4043--4052},
  Volume                   = {84},

  Abstract                 = {We investigate the challenges and limitations that are encountered when studying membrane protein dynamics in vivo by means of fluorescence correlation spectroscopy (FCS). Based on theoretical arguments and computer simulations, we show that, in general, the fluctuating fluorescence has a fractal dimension D(0) >or= 1.5, which is determined by the anomality alpha of the diffusional motion of the labeled particles, i.e., by the growth of their mean square displacement as (Deltax)(2) approximately t(alpha). The fractality enforces an initial power-law behavior of the autocorrelation function and related quantities for small times. Using this information, we show by FCS that Golgi resident membrane proteins move subdiffusively in the endoplasmic reticulum and the Golgi apparatus in vivo. Based on Monte Carlo simulations for FCS on curved surfaces, we can rule out that the observed anomalous diffusion is a result of the complex topology of the membrane. The apparent mobility of particles as determined by FCS, however, is shown to depend crucially on the shape of the membrane and its motion in time. Due to this fact, the hydrodynamic radius of the tracked particles can be easily overestimated by an order of magnitude},
  Doi                      = {10.1016/s0006-3495(03)75130-3},
  Keywords                 = {Algorithms ARE Biology Biophysics Cell Membrane Cells Comparative Study COMPLEXES Computer Simulation CORRELATION SPECTROSCOPY Diffusion DYNAMICS Endoplasmic Reticulum Fluorescence FLUORESCENCE CORRELATION SPECTROSCOPY Fractals Germany Golgi Apparatus Hela Cells Humans IN-VIVO LIVING CELLS Membrane Proteins metabolism methods Microscopy,Confocal Models,Biological Molecular Biology Motion N-Acetylgalactosaminyltransferases physiology Protein Protein Transport Proteins Recombinant Fusion Proteins Research Support,Non-U.S.Gov't Spectrometry,Fluorescence spectroscopy Statistics SURFACE Tissue Distribution ultrastructure},
  Owner                    = {paul},
  Timestamp                = {2014.01.15}
}

@Article{Widengren1995,
  Title                    = {Fluorescence correlation spectroscopy of triplet states in solution: a theoretical and experimental study},
  Author                   = {Widengren, Jerker and Mets, {\"U}lo and Rigler, Rudolf},
  Journal                  = {The Journal of Physical Chemistry},
  Year                     = {1995},
  Number                   = {36},
  Pages                    = {13368-13379},
  Volume                   = {99},

  Doi                      = {10.1021/j100036a009},
  Owner                    = {paul},
  Timestamp                = {2012.02.20}
}

@Article{Widengren1998,
  Title                    = {Fluorescence correlation spectroscopy as a tool to investigate chemical reactions in solutions and on cell surfaces},
  Author                   = {Widengren, J. and Rigler, R.},
  Journal                  = {Cell Mol Biol (Noisy-le-grand)},
  Year                     = {1998},
  Note                     = {Retrieved from \url{http://europepmc.org/abstract/MED/9764752}},
  Number                   = {5},
  Pages                    = {857--79},
  Volume                   = {44},

  Abstract                 = {Taking advantage of the present day possibilities for ultrasensitive detection by fluorescence, fluorescence correlation spectroscopy (FCS) has over the last ten years emerged as a potentially very powerful technique. In this article we present some results to illustrate the use of FCS for monitoring chemical kinetics on a molecular level and show how, for a wide range of chemical processes, the theoretical treatment can be strongly simplified. The experimental examples given include measurements of ion concentrations and buffer properties, electron transfer reactions, ligand-receptor interactions and diffusion of ligand-receptor complexes in cell membranes. For each of these examples the properties of the FCS technique is discussed in relation to other established techniques used for that particular application. From these examples it is found that FCS can offer important complementary information and, due to the extreme sensitivity of the technique, new information not yet explored by other methods.},
  Owner                    = {paul},
  Timestamp                = {2014.01.15}
}

@Article{Widengren1994,
  Title                    = {Triplet-state monitoring by fluorescence correlation spectroscopy},
  Author                   = {Widengren, Jerker and Rigler, Rudolf and Mets, {\"U}lo},
  Journal                  = {Journal of Fluorescence},
  Year                     = {1994},
  Pages                    = {255-258},
  Volume                   = {4},

  Affiliation              = {Department of Medical Biochemistry and Biophysics Karolinska Institute S-171 77 Stockholm Sweden},
  Doi                      = {10.1007/BF01878460},
  ISSN                     = {1053-0509},
  Issue                    = {3},
  Keyword                  = {Biomedizin & Life Sciences},
  Owner                    = {paul},
  Publisher                = {Springer Netherlands},
  Timestamp                = {2012.09.24}
}

@Article{Wohland2001,
  Title                    = {The Standard Deviation in Fluorescence Correlation Spectroscopy},
  Author                   = {Wohland, Thorsten and Rigler, Rudolf and Vogel, Horst},
  Journal                  = {Biophysical Journal},
  Year                     = {2001},

  Month                    = jun,
  Number                   = {6},
  Pages                    = {2987--2999},
  Volume                   = {80},

  Doi                      = {10.1016/S0006-3495(01)76264-9},
  ISSN                     = {0006-3495},
  Owner                    = {paul},
  Timestamp                = {2012.09.08}
}

@Article{Wohland2010,
  Title                    = {Single Plane Illumination Fluorescence Correlation Spectroscopy (SPIM-FCS) probes inhomogeneous three-dimensional environments},
  Author                   = {Thorsten Wohland and Xianke Shi and Jagadish Sankaran and Ernst H.K. Stelzer},
  Journal                  = {Optics Express},
  Year                     = {2010},

  Month                    = {May},
  Number                   = {10},
  Pages                    = {10627--10641},
  Volume                   = {18},

  Abstract                 = {The life sciences require new highly sensitive imaging tools, which allow the quantitative measurement of molecular parameters within a physiological three-dimensional (3D) environment. Therefore, we combined single plane illumination microscopy (SPIM) with camera based fluorescence correlation spectroscopy (FCS). SPIM-FCS provides contiguous particle number and diffusion coefficient images with a high spatial resolution in homo- and heterogeneous 3D specimens and live zebrafish embryos. Our SPIM-FCS recorded up to 4096 spectra within 56 seconds at a laser power of 60 \&\#x03BC;W without damaging the embryo. This new FCS modality provides more measurements per time and more, less photo-toxic measurements per sample than confocal based methods. In essence, SPIM-FCS offers new opportunities to observe biomolecular interactions quantitatively and functions in a highly multiplexed manner within a physiologically relevant 3D environment.},
  Doi                      = {10.1364/OE.18.010627},
  Keywords                 = {Fluorescence microscopy; Three-dimensional microscopy; Spectroscopy, fluorescence and luminescence},
  Owner                    = {paul},
  Publisher                = {OSA},
  Timestamp                = {2012.11.07}
}

@Conference{Wright1996,
  Title                    = {Direct Search Methods: Once Scorned, Now Respectable},
  Author                   = {Wright, M.H.},
  Booktitle                = {Numerical Analysis},
  Year                     = {1996},
  Editor                   = {D.F. Griffiths and G.A. Watson},
  Pages                    = {191-208},
  Publisher                = {Addison Wesley Longman, Harlow, UK},

  Owner                    = {paul},
  Timestamp                = {2014.03.31}
}

@Article{Yordanov2009,
  Title                    = {Direct studies of liquid flows near solid surfaces by total internal reflection fluorescence cross-correlation spectroscopy},
  Author                   = {Stoyan Yordanov and Andreas Best and Hans-J\"{u}rgen Butt and Kaloian Koynov},
  Journal                  = {Optics Express},
  Year                     = {2009},

  Month                    = {Nov},
  Number                   = {23},
  Pages                    = {21149--21158},
  Volume                   = {17},

  Abstract                 = {We present a new method to study flow of liquids near solid surface: Total internal reflection fluorescence cross-correlation spectroscopy (TIR-FCCS). Fluorescent tracers flowing with the liquid are excited by evanescent light, produced by epi-illumination through the periphery of a high numerical aperture oil-immersion objective. The time-resolved fluorescence intensity signals from two laterally shifted observation volumes, created by two confocal pinholes are independently measured. The cross-correlation of these signals provides information of the tracers' velocities. By changing the evanescent wave penetration depth, flow profiling at distances less than 200 nm from the interface can be performed. Due to the high sensitivity of the method fluorescent species with different size, down to single dye molecules can be used as tracers. We applied this method to study the flow of aqueous electrolyte solutions near a smooth hydrophilic surface and explored the effect of several important parameters, e.g. tracer size, ionic strength, and distance between the observation volumes.},
  Doi                      = {10.1364/OE.17.021149},
  Keywords                 = {Velocimetry; Fluorescence, laser-induced; Spectroscopy, surface},
  Owner                    = {paul},
  Publisher                = {OSA},
  Timestamp                = {2012.09.21}
}

@Article{Yordanov2011,
  Title                    = {Note: An easy way to enable total internal reflection-fluorescence correlation spectroscopy ({TIR-FCS}) by combining commercial devices for {FCS} and {TIR} microscopy},
  Author                   = {Stoyan Yordanov and Andreas Best and Klaus Weisshart and Kaloian Koynov},
  Journal                  = {Review of Scientific Instruments},
  Year                     = {2011},
  Number                   = {3},
  Pages                    = {036105},
  Volume                   = {82},

  Doi                      = {10.1063/1.3557412},
  Eid                      = {036105},
  Keywords                 = {fluorescence spectroscopy; optical microscopy},
  Numpages                 = {3},
  Owner                    = {paul},
  Publisher                = {AIP},
  Timestamp                = {2012.05.02}
}

@Article{Zhang2007,
  Title                    = {Gaussian approximations of fluorescence microscope point-spread function models},
  Author                   = {Bo Zhang and Josiane Zerubia and Jean-Christophe Olivo-Marin},
  Journal                  = {Applied Optics},
  Year                     = {2007},

  Month                    = {Apr},
  Number                   = {10},
  Pages                    = {1819--1829},
  Volume                   = {46},

  Abstract                 = {We comprehensively study the least-squares Gaussian approximations of the diffraction-limited 2D-3D paraxial-nonparaxial point-spread functions (PSFs)of the wide field fluorescence microscope (WFFM), the laser scanning confocal microscope(LSCM), and the disk scanning confocal microscope (DSCM). The PSFs are expressed using the Debye integral. Under anL$\infty$ constraint imposing peak matching, optimal and near-optimal Gaussian parameters are derived for the PSFs. With anL1 constraint imposing energy conservation, an optimal Gaussian parameter is derived for the 2D paraxial WFFM PSF. We found that (1) the 2D approximations are all very accurate; (2) no accurate Gaussian approximation exists for 3D WFFM PSFs; and (3) with typical pinhole sizes, the 3D approximations are accurate for the DSCM and nearly perfect for the LSCM. All the Gaussian parameters derived in this study are in explicit analytical form, allowing their direct use in practical applications.},
  Doi                      = {10.1364/AO.46.001819},
  Keywords                 = {Numerical approximation and analysis; Microscopy; Confocal microscopy; Fluorescence microscopy; Three-dimensional microscopy},
  Owner                    = {paul},
  Publisher                = {OSA},
  Timestamp                = {2012.09.20}
}

@Book{Rigler:FCSbook,
  Title                    = {Fluorescence Correlation Spectroscopy, Theory and Applications},
  Editor                   = {R. Rigler and E.S. Elson},
  Publisher                = {Springer Berlin Heidelberg},
  Year                     = {2001},
  Edition                  = {1},

  HowPublished             = {Paperback},
  ISBN                     = {978-3540674337},
  Owner                    = {paul},
  Timestamp                = {2012.11.02}
}

