Showing papers on "Resolution (electron density) published in 2007"

Interferometric synthetic aperture microscopy

Abstract: State-of-the-art methods in high-resolution three-dimensional optical microscopy require that the focus be scanned through the entire region of interest. However, an analysis of the physics of the light–sample interaction reveals that the Fourier-space coverage is independent of depth. Here we show that, by solving the inverse scattering problem for interference microscopy, computed reconstruction yields volumes with a resolution in all planes that is equivalent to the resolution achieved only at the focal plane for conventional high-resolution microscopy. In short, the entire illuminated volume has spatially invariant resolution, thus eliminating the compromise between resolution and depth of field. We describe and demonstrate a novel computational image-formation technique called interferometric synthetic aperture microscopy (ISAM). ISAM has the potential to broadly impact real-time three-dimensional microscopy and analysis in the fields of cell and tumour biology, as well as in clinical diagnosis where in vivo imaging is preferable to biopsy.

The background oriented schlieren technique: sensitivity, accuracy, resolution and application to a three-dimensional density field

Abstract: Three-dimensional density information of a double free air jet was acquired using optical tomography. The projections of the density field were measured using the background oriented schlieren method (BOS). Preceding the free jet measurements, the sensitivity, accuracy and resolution of the BOS method were investigated. The sensitivity depends mostly on the focal length of the lens used, the relative position of the object between camera and background and the smallest detectable shift in the image plane. The accuracy was found to be sufficiently high to apply a tomographic reconstruction process. The resolution is determined by the transfer function of the BOS-method. It is not constant and depends on the size of the interrogation windows used for the cross-correlation-algorithm. The reconstruction of the free jet was computed, using filtered back projection. The reconstructed 3D density field shows with good resolution the typical diamond structure of the density distribution in under-expanded free jets.

X-ray computed tomography in Zernike phase contrast mode at 8 keV with 50-nm resolution using Cu rotating anode X-ray source

Abstract: High-resolution X-ray computed tomography (XCT) enables nondestructive 3D imaging of complex structures, regardless of their state of crystallinity. This work describes a sub-50 nm resolution XCT system operating at 8 keV in absorption and Zemike phase contrast modes based on a commercially available Cu rotating anode laboratory X-ray source. The system utilizes a high efficiency reflective capillary condenser lens and high-resolution Fresnel zone plates with an outermost zone width of 35 nm and 700 nm structure height resulting in a spatial resolution better than 50 nm currently. Imaging a fragment of the solid oxide fuel cells (SOFC) with 50 nm resolution is presented as an application example of the XCT technique in materials science and nanotechnology.

Zone-doubling technique to produce ultrahigh-resolution x-ray optics.

Abstract: A method for the fabrication of ultrahigh-resolution Fresnel zone plate lenses for x-ray microscopy is demonstrated. It is based on the deposition of a zone plate material (Ir) onto the sidewalls of a prepatterned template structure (Si) using an atomic layer deposition technique. This results in a doubling of the effective zone density, thus improving the achievable resolution of x-ray microscopes. Test structures with lines and spaces down to 15 nm were resolved in a scanning transmission x-ray microscope at 1 keV photon energy.

Resolution of λ/10 in fluorescence microscopy using fast single molecule photo-switching

Abstract: We demonstrate nanoscale resolution in far-field optical microscopy based on photo-switching of molecules. By enabling, recording and disabling fluorescence from individual labels sequentially, the detection volume is reduced to the size of a single molecule and the diffraction limit is broken. Images of nanostructures milled into a coverslip and tagged by fluorescent proteins could be recorded at 50 nm resolution. Due to the fast and asynchronous image acquisition protocol used in these experiments, we were able to reduce acquisition times to ∼2.5 min, which is two orders of magnitude lower than in previous implementations.

On the application of an experimental multipolar pseudo-atom library for accurate refinement of small-molecule and protein crystal structures.

Abstract: With an increasing number of biomacromolecular crystal structures being measured to ultra-high resolution, it has become possible to extend to large systems experimental charge-density methods that are usually applied to small molecules. A library has been built of average multipole populations describing the electron density of chemical groups in all 20 amino acids found in proteins. The library uses the Hansen & Coppens multipolar pseudo-atom model to derive molecular electron density and electrostatic potential distributions. The library values are obtained from several small peptide or amino acid crystal structures refined against ultra-high-resolution X-ray diffraction data. The library transfer is applied automatically in the MoPro software suite to peptide and protein structures measured at atomic resolution. The transferred multipolar parameters are kept fixed while the positional and thermal parameters are refined. This enables a proper deconvolution of thermal motion and valence-electron-density redistributions, even when the diffraction data do not extend to subatomic resolution. The use of the experimental library multipolar atom model (ELMAM) also has a major impact on crystallographic structure modelling in the case of small-molecule crystals at atomic resolution. Compared to a spherical-atom model, the library transfer results in a more accurate crystal structure, notably in terms of thermal displacement parameters and bond distances involving H atoms. Upon transfer, crystallographic statistics of fit are improved, particularly free R factors, and residual electron-density maps are cleaner.

Efficient fluorescence inhibition patterns for RESOLFT microscopy.

Abstract: By exploiting the saturation of a reversible single photon transition, RESOLFT microscopy is capable of resolving three dimensional structures inside specimen with a resolution that is no longer limited by the wavelength of the light in use. The transition is driven by a spatially varying intensity distribution that features at least one isolated point, line or plane with zero intensity and the resolution achieved depends critically on the field distribution around these zeros. Based on a vectorial analysis of the image formation in a RESOLFT microscope, we develop a method to effectively search for optimal zero intensity point patterns under typical experimental conditions. Using this approach, we derived a spatial intensity distribution that optimizes the focal plane resolution. Moreover, we outline a general strategy that allows optimization of the resolution for a given experimental situation and present solutions for the most common cases in biological imaging.

Imaging interferometric microscopy–approaching the linear systems limits of optical resolution

Abstract: The linear systems optical resolution limit is a dense grating pattern at a λ/2 pitch or a critical dimension (resolution) of λ/4. However, conventional microscopy provides a (Rayleigh) resolution of only ~ 0.6λ/NA, approaching λ/1.67 as NA → 1. A synthetic aperture approach to reaching the λ/4 linear-systems limit, extending previous developments in imaging-interferometric microscopy, is presented. Resolution of non-periodic 180-nm features using 633-nm illumination (λ/3.52) and of a 170-nm grating (λ/3.72) is demonstrated. These results are achieved with a 0.4-NA optical system and retain the working distance, field-of-view, and depth-of-field advantages of low-NA systems while approaching ultimate resolution limits.

A macromolecule in a solvent: adaptive resolution molecular dynamics simulation.

Abstract: The authors report adaptive resolution molecular dynamics simulations of a flexible linear polymer in solution. The solvent, i.e., a liquid of tetrahedral molecules, is represented within a certain radius from the polymer’s center of mass with a high level of detail, while a lower coarse-grained resolution is used for the more distant solvent. The high resolution sphere moves with the polymer and freely exchanges molecules with the low resolution region through a transition regime. The solvent molecules change their resolution and number of degrees of freedom on the fly. The authors show that their approach correctly reproduces the static and dynamic properties of the polymer chain and surrounding solvent.

Scanning holographic microscopy with resolution exceeding the Rayleigh limit of the objective by superposition of off-axis holograms

Abstract: We present what we believe to be a new application of scanning holographic microscopy to superresolution. Spatial resolution exceeding the Rayleigh limit of the objective is obtained by digital coherent addition of the reconstructions of several off-axis Fresnel holograms. Superresolution by holographic superposition and synthetic aperture has a long history, which is briefly reviewed. The method is demonstrated experimentally by combining three off-axis holograms of fluorescent beads showing a transverse resolution gain of nearly a factor of 2.

An Exponential Separation between Regular and General Resolution.

Abstract: Two distinct proofs of an exponential separation between regular resolution and unrestricted resolution are given. The previous best known separation between these systems was quasi-polynomial.

X-ray structure analysis of a metalloprotein with enhanced active-site resolution using in situ x-ray absorption near edge structure spectroscopy

Abstract: X-ray absorption spectroscopy is exquisitely sensitive to the coordination geometry of an absorbing atom and therefore allows bond distances and angles of the surrounding atomic cluster to be measured with atomic resolution. By contrast, the accuracy and resolution of metalloprotein active sites obtainable from x-ray crystallography are often insufficient to analyze the electronic properties of the metals that are essential for their biological functions. Here, we demonstrate that the combination of both methods on the same metalloprotein single crystal yields a structural model of the protein with exceptional active-site resolution. To this end, we have collected an x-ray diffraction data set to 1.4-Å resolution and Fe K-edge polarized x-ray absorption near edge structure (XANES) spectra on the same cyanomet sperm whale myoglobin crystal. The XANES spectra were quantitatively analyzed by using a method based on the multiple scattering approach, which yielded Fe-heme structural parameters with ±(0.02–0.07)-Å accuracy on the atomic distances and ±7° on the Fe–CN angle. These XANES-derived parameters were subsequently used as restraints in the crystal structure refinement. By combining XANES and x-ray diffraction, we have obtained an cyanomet sperm whale myoglobin structural model with a higher precision of the bond lengths and angles at the active site than would have been possible with crystallographic analysis alone.

The Determination of Protonation States in Proteins.

Abstract: The protonation states of aspartic acids and glutamic acids as well as histidine are investigated in four X-ray cases: Ni,Ca concanavalin A at 0.94 A, a thrombin-hirugen binary complex at 1.26 A resolution and two thrombin-hirugen-inhibitor ternary complexes at 1.32 and 1.39 A resolution. The truncation of the Ni,Ca concanavalin A data at various test resolutions between 0.94 and 1.50 A provided a test comparator for the ;unknown' thrombin-hirugen carboxylate bond lengths. The protonation states of aspartic acids and glutamic acids can be determined (on the basis of convincing evidence) even to the modest resolution of 1.20 A as exemplified by our X-ray crystal structure refinements of Ni and Mn concanavalin A and also as indicated in the 1.26 A structure of thrombin, both of which are reported here. The protonation-state indication of an Asp or a Glu is valid provided that the following criteria are met (in order of importance). (i) The acidic residue must have a single occupancy. (ii) Anisotropic refinement at a minimum diffraction resolution of 1.20 A (X-ray data-to-parameter ratio of approximately 3.5:1) is required. (iii) Both of the bond lengths must agree with the expectation (i.e. dictionary values), thus allowing some relaxation of the bond-distance standard uncertainties required to approximately 0.025 A for a '3sigma' determination or approximately 0.04 A for a '2sigma' determination, although some variation of the expected bond-distance values must be allowed according to the microenvironment of the hydrogen of interest. (iv) Although the F(o) - F(c) map peaks are most likely to be unreliable at the resolution range around 1.20 A, if admitted as evidence the peak at the hydrogen position must be greater than or equal to 2.5 sigma and in the correct geometry. (v) The atomic B factors need to be less than 10 A(2) for bond-length differentiation; furthermore, the C=O bond can also be expected to be observed with continuous 2F(o) - F(c) electron density and the C-OH bond with discontinuous electron density provided that the atomic B factors are less than approximately 20 A(2) and the contour level is increased. The final decisive option is to carry out more than one experiment, e.g. multiple X-ray crystallography experiments and ideally neutron crystallography. The complementary technique of neutron protein crystallography has provided evidence of the protonation states of histidine and acidic residues in concanavalin A and also the correct orientations of asparagine and glutamine side chains. Again, the truncation of the neutron data at various test resolutions between 2.5 and 3.0 A, even 3.25 and 3.75 A resolution, examines the limits of the neutron probe. These various studies indicate a widening of the scope of both X-ray and neutron probes in certain circumstances to elucidate the protonation states in proteins.

Crystal structure of human cyclophilin D in complex with its inhibitor, cyclosporin A at 0.96-A resolution.

Abstract: Crystal structure of human cyclophilin D in complex with its inhibitor, cyclosporin A at 0.96-Å resolution Kenji Kajitani, Masahiro Fujihashi, Yukiko Kobayashi, Shigeomi Shimizu, Yoshihide Tsujimoto, and Kunio Miki* 1Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan 2 Laboratory of Molecular Genetics, Department of Medical Genetics, Osaka University Medical School and SORST of JST, Suita, Osaka 565-0871, Japan

Scanning tunneling microscopy for ultracold atoms

Abstract: We propose a versatile experimental probe for cold atomic gases analogous to the scanning tunneling microscope (STM) in condensed matter This probe uses the coherent coupling of a single particle to the system Depending on the measurement sequence, our probe allows us to obtain either the local density and spatial density correlations, with a resolution on the nanometer scale, or the single particle correlation function in real time We discuss applications of this scheme to the various possible phases for a two dimensional Hubbard system of fermions in an optical lattice

Spatial resolution in Bragg-magnified X-ray images as determined by Fourier analysis

Abstract: The spatial resolution of an imaging system is most often experimentally determined by using model objects and idealized imaging conditions. This traditional approach does not properly take into account the influence of noise and the dependence of contrast on the object. The latter influence is essential especially in the case of magnified X-ray images acquired by two fold asymmetric Bragg diffraction. For this phase sensitive technique the application of a criterion for spatial resolution based upon Fourier analysis is shown to provide reliable resolution values in a simple way, overcoming the limitations mentioned above. For the case of Bragg-magnified imaging of an ant leg with 166 fold magnification (effective pixel size 0.094 μm), the physical resolution achieved in the image is found to be 0.4 μm.