Three-dimensional visualizations

When discassing molecular orbitals, three dimensional visualization software mar be very instructive. 

Proprietary systems are available employing Lego type blocks which can be constructed and placed on a baseboard to represent a three-dimensional visualization of the layout. Another system employs aluminum castings of the actual items of equipment and operatives. Cardboard cutouts have been the most commonly used method, particularly with those who rarely plan layouts. 

A diode array detector is well suited to achieve these goals. Full range spectra should be collected for the method development samples and evaluated with two-dimensional or three-dimensional visualization to determine the best detection wavelength. 

Mechanics and ZINDO were used as implemented on the Tektronix CAChe workstation. Although our initial work (ref. 6) included minimizing the Rh—Rh core with ZINDO, we have subsequently found that this approach works just as well with Mechanics alone. The CAChe workstation is particularly well suited to the sort of analysis outlined here, as its superb three-dimensional visualization facilitates understanding of the competing transition states. 

The following examples involve Odyssey simulations of a few minutes duration each that are carried out under active control of the student with full three-dimensional visualization of all molecular motion. 

Udupa, J.K. 1999. Three-dimensional visualization and analysis methodologies A current perspective. Radiographics 19 783-806. 

Analysis tools for three-dimensional visualization need to be developed for various microscopies and materials analysis instrumentation. 

A clear three-dimensional visualization of the means by which a receptor could differentiate between enantiomers was provided by Easson and Stedman in 1933 [25]. They proposed that three (b, c, d) of the four groups (a, b, c, d) linked to a chiral carbon atom were concerned in the process (either by normal valence forces, or by adsorptive or other forces). The receptor possessed three groups b, c and d for maximum physiological effect, the drug molecule must become attached to the receptor in such a manner that the groups b, c and d in the drug coincide respectively with b, c and d in the receptor. Such coincidence can only occur with one of the enantiomorphs and this consequently represents the more active form of the drug . The interaction (5) and non-interaction (6) were illustrated as follows ... 

The model was used to study the advection and dispersion of a trace contaminant load into a low-permeability soil column. An anisotropic case was simulated. The model estimated and showed the spatial distribution of the contaminant plume and visually depicted the concentration values in grayscale. The three-dimensional visualization provided by the model was shown to be very useful for identifying the extent and severity of the soil contamination due to the trace compound load under three different types of input load distribution (point source, line source, and two-point... 

The efficiency problem caused by the three-dimensional intensive computations can be further improved by applying parallel computing technologies, since the ADI method provides enough parallelism. Details of parallelization will be reported in a future paper. The current three-dimensional visualization demonstrates the distribution of solution concentrations. With further extensions of the web-based simulation system, other solute distributions in different phases will be included. 

Lawton, J. A., Estes, M. K., and Prasad, B. V. (1997). Three-dimensional visualization of mRNA release from actively transcribing rotavirus particles. Nat. Struct. Biol. 4, 118-121. 

Fig. 2 Three-dimensional visualizations of pore structures in a random packing sphere clusters on left polyhedral discretizations of the same on right (A) Ns A, z — A (tightest cluster possible) (B) Ns = 6 z = 1.

Nichols, J., P. Rheingans, D. Lothenbach, R. McGeachie, L. Skow and J. McKim. Three-dimensional visualization of physiologically based kinetic model outputs. Environ. Health Perspect. 102 952-956, 1994. 

Scanning electron microscopy (SEM) constitutes one of the older and one of the most widely used instruments for surface analysis. It provides a three-dimensional visual image and, thus, the quantitative analysis is relatively straightforward. 

Crecelius, A.C. et al., Three-dimensional visualization of protein expression in mouse brain structures using imaging mass spectrometry, J. Am. Soc. Mass Spectrom., 16, 1093, 2005. 

To obtain more information, stress-whitened zones were prepared at Section B. For all the rubber-modified specimens, the size of the stress-whitened zone increased from zero at the outer surface to a maximum at the midsection (Section A). Figure 5 shows the whitened zone at Section B of specimen RF5. The whitened zone of RF series specimens can be three-dimensionally visualized, as shown in Figure 6. The shape of the whitened zone is in opposition to that of the plastic zone ahead of a crack tip in dense materials, in which the size of the plastic zone decreases to a minimum at the midsection because of the state of plane strain. At the outer surface there will always be plane stress, and hence the stress in the thickness direction, a, is zero at the surface. Concurrently, plane strain prevails in the interior, thus increasing the a in the interior. It can accordingly be seen that the maximum hydrostatic stress is found at the midsection (Section A). Thus, stress-whitening appears to be due to the hydrostatic stress components rather than the deviatoric stress components. 

Figure 6. Three-dimensional visualization of the stress-whitened zone of RF series specimens.

The visualization of large data sets has special requirements. A typical example area is multivariate image analysis, especially in remote sensing, but hyperspectral imaging is also moving into other fields. Another is three-dimensional visualization of weather systems. 

Single crystal X-ray diffraction enables the determination of atomic positions in the unit cell, allowing a three-dimensional visualization of the structure. Because... 

An alternative approach to the rationalization of reactivity patterns, involving the three-dimensional visualization of molecular electrostatic potential surfaces, has had some success in explaining the results of the nitration of substituted imidazo[l,2-fl]pyridines <85EJM50l>. 

With the added dimension of height, three-dimensional visualizations are better able to show quantitative relationships over a large dynamic range. However, in three-dimensional visualizations, points on the surface can be obscured, and there is no correspondence between the dimensions of the data and the axes of the display, so interactive operations such as point-and-click indexing are more difficult and problematic than with a two-dimensional image. In that sense, different visualizations are complementary, each with its own utilities. 

Paulsen, P.K. and Hasenkam, J.M. 1983. Three-dimensional visualization of velocity profiles in the ascending aorta in dogs, measured with a hot film anemometer. /. Biomech. 16 201-210. 

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