4,622 research outputs found

    Exploiting peak anisotropy for tracking through complex structures

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    Nonparametric tests of structure for high angular resolution diffusion imaging in Q-space

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    High angular resolution diffusion imaging data is the observed characteristic function for the local diffusion of water molecules in tissue. This data is used to infer structural information in brain imaging. Nonparametric scalar measures are proposed to summarize such data, and to locally characterize spatial features of the diffusion probability density function (PDF), relying on the geometry of the characteristic function. Summary statistics are defined so that their distributions are, to first-order, both independent of nuisance parameters and also analytically tractable. The dominant direction of the diffusion at a spatial location (voxel) is determined, and a new set of axes are introduced in Fourier space. Variation quantified in these axes determines the local spatial properties of the diffusion density. Nonparametric hypothesis tests for determining whether the diffusion is unimodal, isotropic or multi-modal are proposed. More subtle characteristics of white-matter microstructure, such as the degree of anisotropy of the PDF and symmetry compared with a variety of asymmetric PDF alternatives, may be ascertained directly in the Fourier domain without parametric assumptions on the form of the diffusion PDF. We simulate a set of diffusion processes and characterize their local properties using the newly introduced summaries. We show how complex white-matter structures across multiple voxels exhibit clear ellipsoidal and asymmetric structure in simulation, and assess the performance of the statistics in clinically-acquired magnetic resonance imaging data.Comment: Published in at http://dx.doi.org/10.1214/10-AOAS441 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

    Controlled assembly of SNAP-PNA-fluorophore systems on DNA templates to produce fluorescence resonance energy transfer

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    The SNAP protein is a widely used self-labeling tag that can be used for tracking protein localization and trafficking in living systems. A model system providing controlled alignment of SNAP-tag units can provide a new way to study clustering of fusion proteins. In this work, fluorescent SNAP-PNA conjugates were controllably assembled on DNA frameworks forming dimers, trimers, and tetramers. Modification of peptide nucleic acid (PNA) with the O6-benzyl guanine (BG) group allowed the generation of site-selective covalent links between PNA and the SNAP protein. The modified BG-PNAs were labeled with fluorescent Atto dyes and subsequently chemo-selectively conjugated to SNAP protein. Efficient assembly into dimer and oligomer forms was verified via size exclusion chromatography (SEC), electrophoresis (SDS-PAGE), and fluorescence spectroscopy. DNA directed assembly of homo- and hetero-dimers of SNAP-PNA constructs induced homo- and hetero-FRET, respectively. Longer DNA scaffolds controllably aligned similar fluorescent SNAP-PNA constructs into higher oligomers exhibiting homo-FRET. The combined SEC and homo-FRET studies indicated the 1:1 and saturated assemblies of SNAP-PNA-fluorophore:DNA formed preferentially in this system. This suggested a kinetic/stoichiometric model of assembly rather than binomially distributed products. These BG-PNA-fluorophore building blocks allow facile introduction of fluorophores and/or assembly directing moieties onto any protein containing SNAP. Template directed assembly of PNA modified SNAP proteins may be used to investigate clustering behavior both with and without fluorescent labels which may find use in the study of assembly processes in cells

    Rotational dynamics of optically trapped polymeric nanofibers

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    The optical trapping of polymeric nanofibers and the characterization of the rotational dynamics are reported. A strategy to apply a torque to a polymer nanofiber, by tilting the trapped fibers using a symmetrical linear polarized Gaussian beam is demonstrated. Rotation frequencies up to 10 Hz are measured, depending on the trapping power, the fiber length and the tilt angle. A comparison of the experimental rotation frequencies in the different trapping configurations with calculations based on optical trapping and rotation of linear nanostructures through a T-Matrix formalism, accurately reproduce the measured data, providing a comprehensive description of the trapping and rotation dynamics.Comment: (21 pages, 5 figures

    A Low Temperature Nonlinear Optical Rotational Anisotropy Spectrometer for the Determination of Crystallographic and Electronic Symmetries

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    Nonlinear optical generation from a crystalline material can reveal the symmetries of both its lattice structure and underlying ordered electronic phases and can therefore be exploited as a complementary technique to diffraction based scattering probes. Although this technique has been successfully used to study the lattice and magnetic structures of systems such as semiconductor surfaces, multiferroic crystals, magnetic thin films and multilayers, challenging technical requirements have prevented its application to the plethora of complex electronic phases found in strongly correlated electron systems. These requirements include an ability to probe small bulk single crystals at the micron length scale, a need for sensitivity to the entire nonlinear optical susceptibility tensor, oblique light incidence reflection geometry and incident light frequency tunability among others. These measurements are further complicated by the need for extreme sample environments such as ultra low temperatures, high magnetic fields or high pressures. In this review we present a novel experimental construction using a rotating light scattering plane that meets all the aforementioned requirements. We demonstrate the efficacy of our scheme by making symmetry measurements on a micron scale facet of a small bulk single crystal of Sr2_2IrO4_4 using optical second and third harmonic generation.Comment: 8 pages, 5 figure

    A three-dimensional simulation of transition and early turbulence in a time-developing mixing layer

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    The physics of the transition and early turbulence regimes in the time developing mixing layer was investigated. The sensitivity of the mixing layer to the disturbance field of the initial condition is considered. The growth of the momentum thickness, the mean velocity profile, the turbulence kinetic energy, the Reynolds stresses, the anisotropy tensor, and particle track pictures of computations are all examined in an effort to better understand the physics of these regimes. The amplitude, spectrum shape, and random phases of the initial disturbance field were varied. A scheme of generating discrete orthogonal function expansions on some nonuniform grids was developed. All cases address the early or near field of the mixing layer. The most significant result shows that the secondary instability of the mixing layer is produced by spanwise variations in the straining field of the primary vortex structures

    Resonant Elastic Soft X-Ray Scattering

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    Resonant (elastic) soft x-ray scattering (RSXS) offers a unique element, site, and valence specific probe to study spatial modulations of charge, spin, and orbital degrees of freedom in solids on the nanoscopic length scale. It cannot only be used to investigate single crystalline materials. This method also enables to examine electronic ordering phenomena in thin films and to zoom into electronic properties emerging at buried interfaces in artificial heterostructures. During the last 20 years, this technique, which combines x-ray scattering with x-ray absorption spectroscopy, has developed into a powerful probe to study electronic ordering phenomena in complex materials and furthermore delivers important information on the electronic structure of condensed matter. This review provides an introduction to the technique, covers the progress in experimental equipment, and gives a survey on recent RSXS studies of ordering in correlated electron systems and at interfaces

    Advanced Fluorescence Microscopy Techniques-FRAP, FLIP, FLAP, FRET and FLIM

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    Fluorescence microscopy provides an efficient and unique approach to study fixed and living cells because of its versatility, specificity, and high sensitivity. Fluorescence microscopes can both detect the fluorescence emitted from labeled molecules in biological samples as images or photometric data from which intensities and emission spectra can be deduced. By exploiting the characteristics of fluorescence, various techniques have been developed that enable the visualization and analysis of complex dynamic events in cells, organelles, and sub-organelle components within the biological specimen. The techniques described here are fluorescence recovery after photobleaching (FRAP), the related fluorescence loss in photobleaching (FLIP), fluorescence localization after photobleaching (FLAP), Forster or fluorescence resonance energy transfer (FRET) and the different ways how to measure FRET, such as acceptor bleaching, sensitized emission, polarization anisotropy, and fluorescence lifetime imaging microscopy (FLIM). First, a brief introduction into the mechanisms underlying fluorescence as a physical phenomenon and fluorescence, confocal, and multiphoton microscopy is given. Subsequently, these advanced microscopy techniques are introduced in more detail, with a description of how these techniques are performed, what needs to be considered, and what practical advantages they can bring to cell biological research

    Nematic liquid crystal alignment on chemical patterns

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    Patterned Self-Assembled Monolayers (SAMs) promoting both homeotropic and planar degenerate alignment of 6CB and 9CB in their nematic phase, were created using microcontact printing of functionalised organothiols on gold films. The effects of a range of different pattern geometries and sizes were investigated, including stripes, circles and checkerboards. EvanescentWave Ellipsometry was used to study the orientation of the liquid crystal (LC) on these patterned surfaces during the isotropic-nematic phase transition. Pretransitional growth of a homeotropic layer was observed on 1 ¹m homeotropic aligning stripes, followed by a homeotropic mono-domain state prior to the bulk phase transition. Accompanying Monte-Carlo simulations of LCs aligned on nano-patterned surfaces were also performed. These simulations also showed the presence of the homeotropic mono-domain state prior to the transition.</p
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