Cutting artifacts

SEM Emission of secondary electrons Topography Cutting artifacts In vacuum... 

Using crystalline dark-field imaging (only diffracted electrons are allowed to contribute to image formation), visibility of cutting artifacts is suppressed because mass thickness effects do not contribute to the image contrast see Fig. 1.43(b). 

For large systems comprising 36,000 atoms FAMUSAMM performs four times faster than SAMM and as fast as a cut-off scheme with a 10 A cut-off distance while completely avoiding truncation artifacts. Here, the speed-up with respect to SAMM is essentially achieved by the multiple-time-step extrapolation of local Taylor expansions in the outer distance classes. For this system FAMUSAMM executes by a factor of 60 faster than explicit evaluation of the Coulomb sum. The subsequent Section describes, as a sample application of FAMUSAMM, the study of a ligand-receptor unbinding process. 

Size cut enhances resolution, optically important aerosol analysis, low artifact potential, particle bounce amenable to automated compositional analysis automated versions available large networks under development... 

A sample of a wooden artifact gives 5.0 disintegrations/min/g carbon. The half-life of carbon-14 is 5730 years, and the activity of C-14 in wood just cut down from a tree is 15.3 disintegrations/min/g carbon. How old is the wooden artifact ... 

Many other filter functions can be designed, e.g. an exponential or a trapezoidal function, or a band pass filter. As a rule exponential and trapezoidal filters perform better than cut-off filters, because an abrupt truncation of the Fourier coefficients may introduce artifacts, such as the annoying appearance of periodicities on the signal. The problem of choosing filter shapes is discussed in more detail by Lam and Isenhour [11] with references to a more thorough mathematical treatment of the subject. The expression for a band-pass filter is H v) = 1 for v j < v < else... 

The reality of the large peak at 37.4 years might be questioned because 37.4 years is a large fraction of 72 years, however it appeared in the Fourier transform of the oxygen isotope ratios of the modern part of the same Sequoia (1749-1975 A.D.) at 33.4 years so we believe it to be real. Furthermore we cut the data sequence from 72 years to 63 years and made its Fourier transform, and found that the 37 year signal remained unaffected, indicating that it is not an artifact of a half harmonic of 72 years. 

The periodic boundary conditions applied in the system have the consequence that one bilayer leaflet can interact in the normal direction with the other leaflet, not only through the contact region in the core of the bilayer, but also through the water phase. To minimise artifacts, one should systematically increase the size of the water phase. However, this is expensive, especially if the main interest is in the behaviour of the lipids. Another solution is to cut off the... 

The simplest method of XRD analysis, used in early studies and described by Tite (1972 286), is the powder diffraction method. A small sample, typically 5-10 mg, is removed from the artifact, either by scraping the surface, cutting... 

To obtain tissue preparations whose constituents were maintained as closely as possible to their state in vivo, the material had to be fixed, i.e. the enzymes inactivated so that cell structures were instantaneously preserved, an almost unattainable ideal. Formalin was the favored fixative, but others (e.g. picric acid), were also employed. Different methods of fixation caused sections to have different appearances. Further artifacts were introduced because of the need to dehydrate the preparations so that they could be stained by dyes, many of which were lipid-soluble organic molecules. Paraffin wax was used to impregnate the fixed, dehydrated material. The block of tissue was then sectioned, originally by hand with a cut-throat razor, and later by a mechanical microtome. The sections were stained and mounted in balsam for examination. Hematoxylin (basophilic) and eosin (acidophilic) (H and E staining) were the commonest stains, giving blue nuclei and pink cytoplasm. Eosinophils in the blood were recognized in this way. 

The pKj values obtained for PCu(II) and PCu(I) are summarized in Table 9. Before discussing what appears to be a clear cut trend, the precision of individual pKa s should first be considered. It has for example been necessary to revise (downwards) the spinach PCu(II) pKa from 5.3 to 4.8 [121]. Plastocyanin is known to denature at or around pH 4.0 and in earlier work the lowest pH used was 4.5, which does not allow as accurate a fit to pK, values. By using a pH-jump method in which the final low pH is attained at the time of stopped-flow mixing (one reactant solution carrying substantially more buffer is allowed to control the pH), it is now possible with some confidence to include data down to pH 4.0. The other uncertainty is in the precision of the pKg for the PCu(I) remote site from a two pK fit. Again the data has to be free from artifacts introduced at... 

The nearly spherical nature of the dimer formed by two monomers of the integrase catalytic core places active sites on respective monomers on opposite sides of the dimer approximately 35 A separates the carboxylate oxygens of Asp64 of each monomer. While we are convinced that the observed dimer is not an artifact or consequence of crystallization, it would seem difficult to reconcile this distance with the observation that, during in vivo strand transfer, cuts on the target DNA occur with a separation of five base pairs, corresponding to 15-20 A in -form DNA. How can a single dimer accomplish this One possibility is that the cuts do not occur simultaneously. One end of the viral DNA could be joined by a reaction at one active site, followed by carefully controlled movement of DNA and protein relative to one another such that the second active site is now positioned five base pairs away from the initial site of strand transfer. It has been proposed, in a variation on this theme, that the first strand-transfer... 

One approach to avoid cluster artifacts is tlie use of periodic boundary conditions (PBCs). Under PBCs, the system being modeled is assumed to be a unit cell in some ideal crystal (e.g., cubic or orthorhombic, see Theodorouo and Suter 1985). In practice, cut-off distances are usually employed in evaluating non-bonded interactions, so the simulation cell need be surrounded by only one set of nearest neighbors, as illustrated in Figure 3.6. If tlie trajectory of an individual atom (or a MC move of that atom) takes it outside tlie boundary of the simulation cell in any one or more cell coordinates, its image simultaneously enters the simulation cell from tlie point related to the exit location by lattice symmetry. 

As already noted in Chapter 2, for electrostatic interactions, Ewald sums are generally to be preferred over cut-offs because of tlie long-range nature of the interactions. For van der Waals type terms, cut-offs do not introduce significant artifacts provided they are reasonably large (typically 8-12 A). 

Suppose that you measure the intensity of radiation from carbon-14 in an ancient piece of wood to be 6 percent of what it would be in a freshly cut piece of wood. How old is this artifact ... 

Fig. 3.1 The shapes and patterns of some pleasing designs found in nature or constructed as artifacts (a) the flower of the black-eyed Susan. RmJbetkia hirin, lb) the flower, stem, and leaves of the black-eyed Susan (c) a red eft, Notophtluilrrws vintlescens (d) a cut diamond (c) a paisley tie (f) a snail shell. Cepea ne/noralis (g) a monarch butterfly, Daniws plexippiix (h) a suspension bridge. Which are truly symmetrical ...

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