38 research outputs found

    RecA Filament Migration on a Single-Stranded DNA

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    Particles Size Measurements of Silo le Nano-clusters by Using Fluorescence Correlation Spectroscopy

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    Fluorescence correlation spectroscopy (FCS) is a powerful tool in fundamental and applied science to measure the properties of particles diffusing in a liquid. Important parameters of the diffusive particles; such as the diffusion coefficient, particle size, and viscosity, can be directly measured by using FCS with high accuracy. Here, we used FCS to study nano-clusters of silole molecules formed by aggregation in acetone-water mixtures. The analysis of the auto-correlation of the intensity fluctuation from fluorescing nanoaggregates freely diffusing in a solution allowed the determination of the size of the clusters on a nanometer scale. Aggregate formation of silole molecules was investigated systematically by measuring the cluster sizes made at different silole concentrations and water contents

    Rubbed Polyimide Surface Studied by Sum-Frequency Vibrational Spectroscopy

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    Characterization of Noise in a Single-Molecule Fluorescence Signal

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    Single-molecule fluorescence experiments allow monitoring of the structural change and dynamics of a single biomolecule in real time using dye molecules attached to the molecule. Often, the molecules are immobilized on the surface to observe a longer molecular dynamics, yet the finite photon budget available from an individual dye molecule before photobleaching sets the limit to the relatively poor signal-to-noise level. To increase the accuracy of these single-molecule experiments, it is necessary to study the cause of noise in the fluorescence signal from the single molecules. To find the origin of this noise, the lifetime of the fluorescent dye molecules labeled on surface-immobilized DNA was measured by using time-correlation single photon counting. The standard deviation of the fluorescence lifetimes obtained from repeated measurements of a single dye molecule with the total photon number N decreased as 1/N, thus following a shot noise of the Poisson statistics. On the other hand, an additional constant noise source, which is independent of the photon number, was observed from the lifetime uncertainties from many molecules and became more dominant after a certain photon number N. This trend was also followed in the uncertainties of the single-molecule FRET signals obtained from single and many molecules. This additional noise is considered to come from the inhomogeneous environment of each DNA immobilized on the surface. Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.BN/Chirlmin Joo La

    Salt Promotes Protonation of Amine Groups at Air/Water Interface

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    Interfacial water reorientation caused by charged Langmuir monolayers consisting of primary fatty amine (ODA) and cationic lipid having quaternary amine headgroup (DPTAP) were investigated by interface-selective vibrational sum-frequency generation spectroscopy. For DPTAP monolayer, initially large sum-frequency intensity from interfacial water OH band decreased steadily by increasing monovalent salt (NaCl, NaI) concentration due to counterion adsorption. On the other hand, ODA/water exhibited significantly smaller sum-frequency intensity than DPTAP/water, implying only small portion of protonated amine group (−NH<sub>3</sub><sup>+</sup>) initially existed. By increasing the ionic strength, however, SF intensity of water OH band was enhanced markedly up to ∼1 mM, and then decreased in both NaCl and NaI solutions. By measuring the phase of the sum-frequency spectra, it was found that water dipoles under the ODA headgroup point downward, indicating that the surfaces were always positively charged. This demonstrated that increasing ionic strength facilitates protonation of primary amine headgroups. A simple model based on Poisson–Boltzmann (PB) theory explained this protonation behavior of primary amines

    Systematic investigation of coupling between symmetric and antisymmetric stretches of D2O in CHCl3 by 2D IR

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    The coupling between the symmetric (v(s)) and antisymmetric (v(a)) OD stretch modes of monomeric D2O in CHCl3 is investigated using polarization-dependent two-dimensional infrared (2D IR) spectroscopy supported by numerical 2D IR simulations based on the exciton-band theory. The relationship between the local modes&apos; and the exciton states&apos; parameters is systematically studied, including center frequencies, diagonal anharmonicities, coupling, and off-diagonal anharmonicity. The mean coupling between v(s) and v(a) is accurately evaluated to be -49.96 +/- 0.14 cm(-1). The degree of relaxation in the harmonic approximation is quantified, and the angle between the exciton-state dipoles is accurately evaluated to be 101.4 degrees +/- 3.6 degrees. In addition, the effect of the local-mode frequency correlation on the resulting exciton-state frequency correlation and the spectral shape of the linear and 2D IR spectra are also investigated
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