Active alignment

Registration The active alignment of the various pieces of a mold by tabs or locator pins, so that no portion of the mold will stray from the position it was in when it was initially formed around a specimen. 

He and Dai [86a] prepared aligned SWCNT-DNA sensors by chemically coupling ssDNA probes on both the tip and wall of plasma-activated aligned carbon nanotubes on gold electrodes. 

In virtually aU cases the modulator has two fiber attachments, instead of the one the diode laser required. The fiber coupling loss in lithium niobate is low because the waveguide mode is reasonably closely matched to the fiber mode. However, active alignment is still required, which today is done manually. Automated fiber attachment equipment is in development to eliminate this labor intensive, and hence costly, step. 

Figure 29 (a) Detection of a metal ion in the presence of surfactants using the vertically active aligned nanowires, (b) Closed ... 

A piezo-composite consists of a piezoelectric active phase and a passive plastic phase [2]. In the 1-3-configuration adopted in our case, piezoelectric rods parallely aligned in thickness direction are imbedded in a three-dimensional plastic matrix (Fig. 1). The distance between the rods has to be chosen inferior to the half wave length of the shear wave in the matrix material ensuring that the whole compound is vibrating as a quasi-homogeneous material. 

After an alignment of a set of molecules known to bind to the same receptor a comparative molecular field analysis CoMFA) makes it possible to determine and visuahze molecular interaction regions involved in hgand-receptor binding [51]. Further on, statistical methods such as partial least squares regression PLS) are applied to search for a correlation between CoMFA descriptors and biological activity. The CoMFA descriptors have been one of the most widely used set of descriptors. However, their apex has been reached. 

Fig. 10.12 Sequence alignment of trypsin, chymotrypsin and thrombin (bovine). The active sites histidine, aspartic acid and serine are highlighted.

Figure 1.2. Endo and exo pathway for the Diels-Alder reaction of cyclopentadiene with methyl vinyl ketone. As was first noticed by Berson, the polarity of the endo activated complex exceeds that of the exo counterpart due to alignment of the dipole moments of the diene and the dienophile K The symmetry-allowed secondary orbital interaction that is only possible in the endo activated complex is usually invoked as an explanation for the preference for endo adduct exhibited by most Diels-Alder reactions.

In 1961 Berson et al. were the first to study systematically the effect of the solvent on the endo-exo selectivity of the Diels-Alder reaction . They interpreted the solvent dependence of the endo-exo ratio by consideririg the different polarities of the individual activated complexes involved. The endo activated complex is of higher polarity than the exo activated complex, because in the former the dipole moments of diene and dienophile are aligned, whereas in the latter they are pointing in... 

Once the molecules are aligned, a molecular field is computed on a grid of points in space around the molecule. This field must provide a description of how each molecule will tend to bind in the active site. Field descriptors typically consist of a sum of one or more spatial properties, such as steric factors, van der Waals parameters, or the electrostatic potential. The choice of grid points will also affect the quality of the final results. 

The functionality available in MedChem Explorer is broken down into a list of available computational experiments, including activity prediction, align/ pharmacophore, overlay molecules, conformer generation, property calculation, and database access. Within each experiment, the Web system walks the user through a series of questions that must be answered sequentially. The task is then submitted to a remote server, where it is performed. The user can view the progress of the work in their Web browser at any time. Once complete, the results of the calculation are stored on the server. The user can then run subsequent experiments starting with those results. The Web interface includes links to help pages at every step of the process. 

The biggest limitation of the CoMFA method is the alignment step. The algorithm superimposes the portions of the inhibitors that are of similar stmcture, assuming that they bind with similar orientations in the active site of the enzyme, which is not necessarily the case. Also, because of a problem with alignment, a CoMFA may fail when a few molecules are very dissimilar from all others in the series. Like QSAR, CoMFA does not require a stmcture of the relevant biological receptor, but does require knowledge about a series of inhibitory compounds. 

Fig. 25-2. Double-beam, double-pass transmissometer for measuring smoke density in stacks. A[, chopper wheel A, beam gating wheel A3, aperture D, detector Fj, spectral filter F2, solenoid-activated neutral density filter L, lamp M, half-mirror/beam splitter Rj, solenoid-activated zero calibration reflector R2, retroreflector (alignment bullseye not shown). Design patented. Source Drawing courtesy of Lear Siegler, Inc.

Zvelebil, M.J., et al. Prediction of protein secondary structure and active sites using the alignment of homologous sequences. /. Mol. Biol. 195 957-961, 1987. 

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