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Dynamic analysis of a diffusing particle in a trapping potential

Lindner, M. (author), Nir, G. (author), Vivante, A. (author), Young, I.T. (author), Garini, Y. (author)

The dynamics of a diffusing particle in a potential field is ubiquitous in physics, and it plays a pivotal role in single-molecule studies. We present a formalism for analyzing the dynamics of diffusing particles in harmonic potentials at low Reynolds numbers using the time evolution of the particle probability distribution function. We...

journal article 2013

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HU Protein Induces Incoherent DNA Persistence Length

Nir, G. (author), Lindner, M. (author), Dietrich, H.R.C. (author), Girshevitz, O. (author), Vorgias, C.E. (author), Garini, Y. (author)

HU is a highly conserved protein that is believed to play an important role in the architecture and dynamic compaction of bacterial DNA. Its ability to control DNA bending is crucial for functions such as transcription and replication. The effects of HU on the DNA structure have been studied so far mainly by single molecule methods that require...

journal article 2011

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Force-free measurements of the conformations of DNA molecules tethered to a wall

Lindner, M. (author), Nir, G. (author), Medalion, S. (author), Dietrich, H.R.C. (author), Rabin, Y. (author), Garini, Y. (author)

Using an optimized combination of tethered particle motion method, total internal reflection, and a gold nanobead, we measured the three-dimensional distribution of the free end of a tethered DNA molecule. The distribution along the axial z direction (perpendicular to the surface) is found to be Rayleigh-like, in agreement with wormlike chain...

journal article 2011

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Transient Anomalous Diffusion of Telomeres in the Nucleus of Mammalian Cells

Bronstein, I. (author), Israel, Y. (author), Kepten, E. (author), Mai, S. (author), Shav-Tal, Y. (author), Barkai, E. (author), Garini, Y. (author)

We measured individual trajectories of fluorescently labeled telomeres in the nucleus of eukaryotic cells in the time range of 10-2–104 sec by combining a few acquisition methods. At short times the motion is subdiffusive with (r2)?t? and it changes to normal diffusion at longer times. The short times diffusion may be explained by the reptation...

journal article 2009

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Tethered particle motion mediated by scattering from gold nanoparticles and darkfield microscopy

Dietrich, H.R.C. (author), Rieger, B. (author), Wiertz, F.G.M. (author), De Groote, F.H. (author), Heering, H.A. (author), Young, I.T. (author), Garini, Y. (author)

journal article 2009

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Structured illumination microscopy using extraordinary transmission through sub-wavelength hole-arrays

Docter, M.W. (author), Van den Berg, P.M. (author), Alkemade, P.F.A. (author), Kutchoukov, V.G. (author), Piciu, O.M. (author), Bossche, A. (author), Young, I.T. (author), Garini, Y. (author)

journal article 2007

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A new optical method for characterizing single molecule interactions based on dark field microscopy

Dietrich, H.R.C. (author), Vermolen, B.J. (author), Rieger, B. (author), Young, I.T. (author), Garini, Y. (author)

Single-molecule techniques continue to gain in popularity in research disciplines such as the study of intermolecular interactions. These techniques provide information that otherwise would be lost by using bulk measurements that deal with a large number of molecules. We describe in this report the motion of tethered DNA molecules that have been...

conference paper 2007

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Measuring the wavelength-dependent divergence of transmission through sub-wavelength hole-arrays by spectral imaging

Docter, M.W. (author), Young, I.T. (author), Piciu, O.M. (author), Bossche, A. (author), Alkemade, P.F.A. (author), Van den Berg, P.M. (author), Garini, Y. (author)

We present a study on the far-field patterns of light transmitted through sub-wavelength metallic hole-arrays. Spectral imaging measurements are used here on hole arrays for the first time. It provides both spatial and spectral information of the transmission in far-field. The visibility of the images, measured in two illumination modes: Köhler...

journal article 2006

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Measuring the near-field of extra-ordinary transmission through a periodic hole-array

Docter, M.W. (author), Young, I.T. (author), Piciu, O. (author), Bossche, A. (author), Alkemade, P.F.A. (author), Van de Berg, P.M. (author), Garini, Y. (author)

The knowledge of the near-field of extra-ordinary transmission through hole-arrays is mostly theoretical; there is less experimental validation of the theory. We study the near-field properties by measuring fluorescent molecules that are immersed in a solution and their Brownian motion. The measurements are performed by filling the space above...

conference paper 2006

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Titre plate and measuring device for chemical and/or biochemical analysis

Bossche, A. (author), Kutchoukov, V.G. (author), Garini, Y. (author), Young, I.A. (author)

The invention relates to a titre plate for chemical and/or biochemical analysis based on an illumination measurement comprising a transparent substrate, applied to the substrate there is a metallic layer, which is provided with an array of reaction chambers, wherein the reaction chambers extend from the top side of the metallic layer to, or into...

patent 2006

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Advances in the development of a novel method to be used in proteomics using gold nanobeads

Dietrich, H.R.C. (author), Young, I.T. (author), Garini, Y. (author)

The study of DNA-protein interactions is gaining increased attention due to their importance in cellular processes. Only a well-functioning interaction guaranties that such a process can take place without errors. So far, only a small percentage of these interactions have been unraveled, partially due to their complexity but also due to the fact...

conference paper 2006

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Absolute fluorescence calibration

Young, I.T. (author), Garini, Y. (author), Vermolen, B. (author), Liqui Lund, G. (author), Brouwer, G. (author), Hendrichs, S. (author), El Morabit, M. (author), Spoelstra, J. (author), Wilhelm, E. (author), Zaal, M. (author)

While fluorescence microscope systems remains an essential tool in modern biology and medical work, no compact instrumentation has been developed for the rapid calibration of such systems. Almost invariably results are presented in terms of the [AU], "arbitrary units". To remedy this situation we have developed a small, portable instrument - the...

conference paper 2006

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Optical microscope and method for obtaining an optical image

Garini, Y. (author), Young, I.T. (author)

The invention relates to an optical microscope, comprising, at least a light source, a carrier for an object to be examined, a detector for registering the illuminated object, and a light path that during operation runs substantially from the light source to the object and form the object to the detector, wherein a metallic film having a...

patent 2005

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Adaptation of nanoarrays for the study of ?-synuclein aggregation - preliminary results

Dietrich, H.R.C. (author), Van den Doel, R.L. (author), Hoyer, W. (author), Van Oel, W. (author), Liqui Lung, G. (author), Garini, Y. (author), Jovin, T. (author), Young, I.T. (author)

In previous publications we have shown that we can perform enzymatic reactions in nanoarrays by means of a microarray-reader based on a conventional microscope. In this publication we report on a modification of this system in order to monitor the aggregation kinetics of the natively unfolded protein ?-synuclein. We describe the motivation for...

conference paper 2005

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Three-dimensional analysis tool for segmenting and measuring the structure of telomeres in mammalian nuclei

Vermolen, B.J. (author), Young, I.T. (author), Chuang, A. (author), Wark, L. (author), Chuang, T. (author), Mai, S. (author), Garini, Y. (author)

Quantitative analysis in combination with fluorescence microscopy calls for innovative digital image measurement tools. We have developed a three-dimensional tool for segmenting and analyzing FISH stained telomeres in interphase nuclei. After deconvolution of the images, we segment the individual telomeres and measure a distribution parameter we...

conference paper 2005

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Gold nanoparticles: A novel application of spectral imaging in proteomics - preliminary results

Dietrich, H.R.C. (author), Young, I.T. (author), Garini, Y. (author)

The intense research in proteomics is demanding for fast, reliable and easy-to-use methods in order to study the proteome. In this proceeding we report the development of such a novel research tool based on spectral imaging and Resonance Light Scattering gold particles. This method will allow the study of DNA-protein interactions. We suggest a...

conference paper 2005

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A novel concept for a mid-field microscope

Docter, M.W. (author), Young, I.T. (author), Kutchoukov, V.G. (author), Bossche, A. (author), Alkemade, P.F.A. (author), Garini, Y. (author)

When light passes through a hole smaller than the wavelength of the light, the transmission is very low and the light is diffracted. This however changes if holes are arranged in a periodic array on metal. In that case the light couples to surface plasmons; this results in enhanced transmission, spectral selection and a small angular diffraction...

conference paper 2005

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Optical detection of electrokinetically manipulated single molecules in a nanofluidic chip

Parikesit, G.O.F. (author), Kutchoukov, V.G. (author), Bossche, A. (author), Young, I.T. (author), Garini, Y. (author)

We report on the progress of a novel nanofluidic device for detecting and manipulating single molecules in solution. This paper discusses the development of an earlier proposed molecule separation method, where electrokinetic forces separate different molecules based on their masses and charges. Optical imaging using confocal microscopy is...

conference paper 2005

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Optical detection of single molecules in nanofluidic chips

Parikesit, G.O.F. (author), Kutchoukov, V.G. (author), Van Oel, W. (author), Lung, G.L. (author), Bossche, A. (author), Young, I.T. (author), Garini, Y. (author)

We present the latest progress on a novel technology for detecting and manipulating solution of single molecules in nanofluidic channels. This paper explains the design and fabrication of nanofluidic chip and its interface, molecule manipulation technique being used, and the optical detection method employed. Single molecule detections are...

conference paper 2004

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LEDs for fluorescence microscopy

Young, I.T. (author), Garini, Y. (author), Dietrich, H.R.C. (author), Van Oel, W. (author), Liqui Lung, G. (author)

Traditional light sources for fluorescence microscopy have been mercury lamps, xenon lamps, and lasers. These sources have been essential in the development of fluorescence microscopy but each can have serious disadvantages: lack of near monochromaticity, heat generation, cost, lifetime of the light source, and possible distortions due to...

conference paper 2004