Showing papers on "Resolution (electron density) published in 1993"

Difference imaging of adenovirus: bridging the resolution gap between X-ray crystallography and electron microscopy.

Abstract: While X-ray crystallography provides atomic resolution structures of proteins and small viruses, electron microscopy provides complementary structural information on the organization of larger assemblies at lower resolution. A novel combination of these two techniques has bridged this resolution gap and revealed the various structural components forming the capsid of human type 2 adenovirus. An image reconstruction of the intact virus, derived from cryo-electron micrographs, was deconvolved with an approximate contrast transfer function to mitigate microscope distortions. A model capsid was calculated from 240 copies of the crystallographic structure of the major capsid protein and filtered to the correct resolution. Subtraction of the calculated capsid from the corrected reconstruction gave a three-dimensional difference map revealing the minor proteins that stabilize the virion. Elongated density penetrating the hexon capsid at the facet edges was ascribed to polypeptide IIIa, a component required for virion assembly. Density on the inner surface of the capsid, connecting the ring of peripentonal hexons, was assigned as polypeptide VI, a component that binds DNA. Identification of the regions of hexon that contact the penton base suggests a structural mechanism for previously proposed events during cell entry.

Simultaneous STEM imaging and electron energy-loss spectroscopy with atomic-column sensitivity

Abstract: IMAGING with the scanning transmission electron microscope (STEM) has recently gained in resolution from the use of the annular dark-field (ADF) method1,2, which produces a signal that is highly sensitive to atomic number. There is a possibility that electrons from the probe beam that are scattered inelastically might be collected to provide a spectroscopic signal containing information about atomic bonding and electronic structure—this is the basis of the standard electron energy-loss spectroscopy (EELS) technique. Browning et al.3,4 have shown recently that an EELS signal from absorption of atomic core levels can be used, in con-junction with ADF imaging, to obtain information about chemical composition at atomic resolution. Here I report the use of a similar approach to resolve the different bonding states of silicon atoms (Si0, Si2 + , Si4 +) across a Si–SiO2interface. The oxidation state of individual columns of unit cells, containing pairs of silicon atoms, can be resolved with this method, allowing the structure of the interface to be characterized in great detail.

Picosecond resolution in scanning tunneling microscopy

Abstract: A method has been developed for performing fast time-resolved experiments with a scanning tunneling microscope. The method uses the intrinsic nonlinearity in the microscope's current versus voltage characteristics to resolve optically generated transient signals on picosecond time scales. The ability to combine the spatial resolution of tunneling microscopy with the time resolution of ultrafast optics yields a powerful tool for the investigation of dynamic phenomena on the atomic scale.

Multipole analysis of the electron density in triphylite, LiFePO4, using X-ray diffraction data

Abstract: The electron density distribution and 3d-orbital electron occupancies for the Fe atom in synthetic triphylite, LiFePO 4 , have been analysed using single-crystal X-ray diffraction data measured at T=298 K with Mo Kα (λ=0.71069 A) radiation to a resolution corresponding to (sin θ max /λ)=1.078 A -1 . Measurements of 3265 reflections gave 944 unique data [R int (I)=0.036] with I>2σ(I). For an atomic multipole density model fitted by least-squares methods R(F)=0.0174 for all unique reflections. The Fe atom 3d-orbital occupancies have been derived from the multipole population coefficients using point-group-specific relations

Resolution limits in ray tomography due to wave behavior: Numerical experiments

Abstract: Several factors limit the resolution obtained in ray tomography. Of these the least thoroughly discussed in the geophysical literature is the effect of the ray approximation itself; scattering is ignored and the information contained in a seismic trace is reduced to one traveltime pick. Frequency domain comparisons of ray tomography with diffraction tomography have suggested that the minimum feature size resolvable by ray tomography is of the order of the width of the first Fresnel zone. We investigate resolution in the spacetime domain with a numerical experiment. Four synthetic data sets were generated with a finite‐difference program corresponding to crosshole tomographic surveys at two hole separations and two frequencies. The scale of resolution achieved in tomograms derived from these is then assessed by calculating their semblance to filtered versions of the original model and reconstructions from data sets obtained by tracing rays through the original models. The results broadly confirm the relati...

Spatial resolution of silicon microstrip detectors

Abstract: The spatial resolution of silicon microstrip detectors is studied as a function of the main detector parameters and of the track angle. Several algorithms for finding the position of particle hits are presented and analysed. Analytic expressions of the spatial resolution are derived for the main algorithms. Using a Monte Carlo simulation, the spatial resolution is calculated for each algorithm and, for each detector design and track geometry, the algorithm that gives the best resolution is determined.

Multipole Analysis of the Electron Density in Triphylite LiFePO4 using X-ray Diffraction Data

Abstract: The electron density distribution and 3d-orbital electron occupancies for the Fe atom in synthetic triphylite, LiFePO 4 , have been analysed using single-crystal X-ray diffraction data measured at T=298 K with Mo Kα (λ=0.71069 A) radiation to a resolution corresponding to (sin θ max /λ)=1.078 A -1 . Measurements of 3265 reflections gave 944 unique data [R int (I)=0.036] with I>2σ(I). For an atomic multipole density model fitted by least-squares methods R(F)=0.0174 for all unique reflections. The Fe atom 3d-orbital occupancies have been derived from the multipole population coefficients using point-group-specific relations

Microscale elastic‐strain determination by backscatter Kikuchi diffraction in the scanning electron microscope

Abstract: It is shown that backscatter Kikuchi diffraction in the scanning electron microscope can be used for the determination of elastic strain with μm resolution. From the shift of Kikuchi bands in backscatter Kikuchi diffraction patterns of epitaxial Si1−xGex layers on Si(100) the perpendicular elastic strain was determined to be 2.5% for x=0.34 and at 1.0% for x=0.16 with an accuracy of about 0.1%. The values found on a μm scale were in good agreement with high‐resolution x‐ray diffraction measurements averaging over mm distances.

Ultrafast scanning probe microscopy

Abstract: We have measured the response of the tunneling gap of a scanning tunneling microscope to excitation by a subpicosecond electrical pulse. Combining ultrashort laser pulses techniques with scanning tunneling microscopy (STM), we have obtained simultaneous 2‐ps time resolution and 50‐A spatial resolution. This is a 9 orders of magnitude improvement in the time resolution currently attainable with STM. The potential of this powerful technique for studying ultrafast dynamical phenomena on surfaces with atomic resolution and mesoscopic electronic device physics is discussed.

The convergence of object dependent resolution in maximum likelihood based tomographic image reconstruction

Abstract: Study of the maximum likelihood by EM algorithm (ML) with a reconstruction kernel equal to the intrinsic detector resolution and sieve regularization has demonstrated that any image improvements over filtered backprojection (FBP) are a function of image resolution. Comparing different reconstruction algorithms potentially requires measuring and matching the image resolution. Since there are no standard methods for describing the resolution of images from a nonlinear algorithm such as ML, the authors have defined measures of effective local Gaussian resolution (ELGR) and effective global Gaussian resolution (EGGR) and examined their behaviour in FBP images and in ML images using two different measurement techniques. For FBP these two resolution measures are equal and exhibit the standard convolution behaviour of linear systems.

High resolution neutron powder diffraction: a case study of the structure of C60

Abstract: High resolution time-of-flight neutron powder diffraction has been used to determine the detailed structure of C$\_{60}$ as a function of temperature. Rapid data collection coupled with high resolution has enabled subtle aspects of the 86 K orientational glass transition and precursor effects of the 260 K order-disorder transition to be observed. This surveying capability complements traditional single crystal methods. The power of the Rietveld method of profile refinement is demonstrated in the elucidation of the detailed crystal structure of the orientationally-ordered low temperature phase and in the evaluation of the departure from isotropic scattering of the C$\_{60}$ molecule in the disordered high temperature phase. The counter-intuitive success in obtaining high-order cubic-harmonic coefficients, albeit to poorer precision than single crystal X-ray measurements, confirms the efficacy of the Rietveld profile refinement method. The collapse of three dimensions of diffraction information on to the one dimension of a high resolution powder diffraction pattern can still lead to an impressive amount of structural information that substantiates the assertion made by W. H. Bragg `the second method [powder diffraction], first used independently by Debye and Hull, can be used when the crystal is in powder, and can, therefore be employed when no single crystal can be obtained of sufficient size. All the spectra of the different planes are thrown together on the same diagram or photograph, and must be disentangled. This is not as difficult as it may seem...'.

Contact faces of epitaxially crystallized .alpha.- and .gamma.-phase isotactic polypropylene observed by atomic force microscopy

Abstract: The structure and contact faces of epitaxially crystallized isotactic polypropylene (iPP) in its α and γ phases are investigated by electron microscopy, electron diffraction, and atomic force microscopy (AFM). AFM results with methyl group resolution help recognize which one of two possible contact faces interacts with the substrate. Structural analysis makes it possible (at least in the a phase) to determine the hand of helices in contact with the substrate

The structure of a centrosymmetric protein crystal.

Abstract: Crystals of racemic rubredoxin, prepared by independent chemical synthesis of the two enantiomers, have been grown and characterized. The unit cell contains two molecules, one of each enantiomer. Examination of the intensity distribution in the diffraction pattern revealed that the crystals are centrosymmetric. This was confirmed by solution of thestructure to 2 A resolution via molecular replacement methods. The electron density maps are of very high quality due to the fact that the phaseof each reflection must be exactly 0° or exactly 180°. These results demonstrate the feasibility of using synthetic racemic proteins to yield centrosymmetric protein crystals with electron density maps that have very low phase error and model bias. © 1993 Wiley-Liss, Inc.

Atomic Resolution with Atomic Force Microscope

Abstract: The atomic force microscope (AFM) is a promising new method for studying the surface structure of both conductors and insulators. In mapping a graphite surface with an insulating stylus, we have achieved a resolution better than 2.5 A.

Resolution limits in electron-beam induced tungsten deposition

Abstract: Electron‐beam induced deposition of tungsten from the precursor gas W(CO)6 was investigated with the aim of determining the resolution limiting parameters. By exploring the effect of the beam energy and current, the resolution was found to correlate to the expected behavior of the beam diameter. To achieve a more accurate description of the deposition process, the time dependence of the needle height and diameter at the base was determined for deposition times ranging from 5 to 180 s. The measurements enabled a mathematical description of the needle surface as a function of time, and, therefore, the determination of the surface growth. The results exhibit that electron scattering cannot explain the observed growth. For that reason, the surface growth was correlated to the number of secondary electrons (SE) emitted by the primary e beam from the needle surface considering the Gaussian intensity distribution of the e beam and the angle dependence of the SE yield. These assumptions result in a good agreement of the number of SE with the surface growth and demonstrate that the beam diameter mainly limits the deposit resolution. As a consequence, by using a proper e‐beam system, a resolution of 1 μm high needles in the order of 50 nm is obtainable.

Scanning luminescence X‐ray microscopy: Imaging fluorescence dyes at suboptical resolution

Abstract: Scanning luminescence X‐ray microscopy is based on the use of the very small focused probe of a scanning X‐ray microscope to stimulate visible light emission from phosphors and dyes. Using an undulator X‐ray source and a Fresnel zone plate to produce a focused X‐ray probe, images of P31 phosphor grains with a resolution of 50–75 nm have been obtained, and luminescence from polystyrene spheres loaded with 50–100 μmol/g of fluorescent dye has been imaged. The resolution was not limited by the focused X‐ray probe (the microscope has imaged features at 36‐nm spacing in transmission mode) but by dark noise and the low net efficiency of the luminescence detection system used for this investigation. This technique may make it possible to image dye‐tagged sites of biochemical activity at the resolution of the X‐ray microscope in wet, unsectioned, and unfixed cells, especially with soft X‐ray optimized dyes. Because the image is formed from the detection of signal against a dark background, calculations suggest that the radiation dose for luminescence imaging of dye‐tagged features should be 2–22 times lower than it is in transmission X‐ray microscopy. A possible extension of the technique for three‐dimensional imaging at the transverse resolution of the X‐ray microscope is described, where visible light collection optics might be used to obtain submicrometre axial resolution.

Simultaneous Correction of Attenuation and Distance-dependent Resolution in Spect - An Analytical Approach

Abstract: An approximate analytical solution of the problem of attenuation and distance-dependent resolution effects in single photon emission tomography is presented for the case of a uniform absorbing medium. The algorithm obtained is a generalization of the Bellini and co-workers formula correcting for the single attenuation effect and is derived by means of Fourier transforms only. The method has been validated on mathematical phantoms as well as on physical data.

Resolution in collection-mode scanning optical microscopy

Abstract: The use of small apertures or sharpened tips as sensing elements in scanned‐probe optical sensing devices has led to the development of a number of instruments that provide lateral spatial resolution much finer than that available in conventional optical imaging instruments. Such a device might generally be classified as a scanning optical microscope, or SOM. One particular mode of SOM operation involves the use of a sharpened optical fiber to collect light emanating from a surface. The lateral spatial resolution of such a collection‐mode SOM is discussed in terms of the electromagnetic mode solutions of the probe tip. Numerical results indicate that, though bound modes solutions exist for increasingly fine unclad tips, classical diffraction effects limit resolution to a finite fraction (approximately 1/3) of the source wavelength λ. A second mechanism for signal transduction is shown to involve molecular scattering at the probe tip. An analysis of signal collection efficiency demonstrates that at tip radii below λ/5 for metallic‐clad probes, and λ/10 for probes in a dielectric ambient, scattering dominates and imaging resolution scales with tip size, thus defeating limits imposed by diffraction.

Excitation field synthesis as a means for obtaining enhanced axial resolution in fluorescence microscopes

Abstract: For fundamental reasons, fluorescence microscopes are more limited in axial, as opposed to transverse, resolution. By giving the excitation field a particular axial structure, this limitation can be partially alleviated, as in confocal scanning or two-photon scanning, or even in optical sectioning microscopy in cases where the object occupies only a small part of the field of view. Standing-wave fluorescence microscopy (SWFM) is a direct imaging method in which the specimen is excited by a 3-D field of planar interference fringes oriented parallel to the object focal plane of the microscope. By shifting the position of the nodal planes of this field relative to the specimen, structures that are normally obscured under uniform excitation become resolved. We demonstrate that, in very thin biological specimens, this optical subsectioning increases axial resolution by an order of magnitude, to 0.04 μm. In comparison to confocal scanning, SWFM resolves fine axial structure with more than 10-fold greater speed, and with similarly-reduced photobleaching. We also discuss the more general case of excitation field synthesis (EFS), in which standing wave fields differing in node spacing can be overlapped or time-multiplexed in the specimen so that the average field is non-periodic and peaked at the object focal plane. A transfer function model is given to show that for weakly-refractive specimens of arbitrary thickness, such as single cells or cell monolayers, EFS should lead to a fivefold improvement in axial resolution.