Helical simulation

To date, RNA calculations have been performed on a variety of systems of different topologies including helical duplexes, hairpin loops, and single strands from tRNA, rRNA, and ribozymes. In a simulation of an RNA tetraloop of the GRNA type, which is very common and known to be remarkably stable, it was found that without imposing any external infonnation the simulation found the right confonnation even when it started from the wrong one [72]. Studies have used Ewald summation methods to handle the... 

Figure 18.14 The diffraction pattern of helices in fiber crystallites can be simulated by the diffraction pattern of a single slit with the shape of a sine curve (representing the projection of a helix). Two such simulations are given in (a) and (b), with the helix shown to the left of its diffraction pattern. The spacing between the layer lines is inversely related to the helix pitch, P and the angle of the cross arms in the diffraction pattern is related to the angle of climb of the helix, 6. The helix in (b) has a smaller pitch and angle of climb than the helix in (a). (Courtesy of W. Fuller.)...

The toroidal and helical forms that we consider here are created as such examples these forms have quite interesting geometrical properties that may lead to interesting electrical and magnetic properties, as well as nonlinear optical properties. Although the method of the simulations through which we evaluate the reality of the structure we have imagined is omitted, the construction of toroidal forms and their properties, especially their thermodynamic stability, are discussed in detail. Recent experimental results on toroidal and helically coiled forms are compared with theoretical predictions. 

Here, ry is the separation between the molecules resolved along the helix axis and is the angle between an appropriate molecular axis in the two chiral molecules. For this system the C axis closest to the symmetry axes of the constituent Gay-Berne molecules is used. In the chiral nematic phase G2(r ) is periodic with a periodicity equal to half the pitch of the helix. For this system, like that with a point chiral centre, the pitch of the helix is approximately twice the dimensions of the simulation box. This clearly shows the influence of the periodic boundary conditions on the structure of the phase formed [74]. As we would expect simulations using the atropisomer with the opposite helicity simply reverses the sense of the helix. 

Additional patterns have been simulated, including near 0 to about 90 helices. Test cylinders have also been wound with roving. The graphical presentation is effective for conformation before winding and demonstrates the successful development of a numericeiUy controlled, filament winder. 

Fig. 2.36 The y-peptide 2.614-helical fold. (A) Stereo-view along the helix axis of the (P)-2.6i4-helical structure adopted by y -hexapep-tide 141 in pyridine. This low energy confor-mer was obtained by simulated annealing calculations under NMR restraints. Side-chains have been partially omitted for clarity.

ScHONEELD, F., Haedt, S., Simulation of helical flows in microchannels, AlChE J. (2003) accepted for publication. 

These low-temperature amide V IR and VCD isotope-edited results could be modeled with near-quantitative accuracy with DFT parameters by transferring ab initio FF, APT, and AAT parameters from computations for an a -helical heptapeptide model compound onto an o -helical 20-mer oligopeptide (Fig. 8 left). This simulation does not agree with data for the C-terminally labeled oligomer, because experimentally that end of... 

Fig. 8. Theoretical simulation of VCD (top) and IR absorption (bottom) spectra of alanine dodecapeptides for the amide V bands for a fully a-helical conformation (left) and a fully left-handed 3i-helical conformation (right). The simulations are for the same three isotopically labeled (13C on the amide C=0 for four Ala residues selected in sequence) peptides as in Figure 7 N-terminal tetrad (4AL1), middle (4AL2), and C-terminal (4AL4). The 13C feature is the same for all sequences, confirming the experimentally found unfolding of the C-terminus. The agreement with the shapes in Figure 7 is near quantitative. Reprinted from Silva, R. A. G. D., Kubelka, J., Decatur, S. M., Bour, R, and Keiderling, T. A. (2000a). Proc. Natl. Acad. Sci. USA 97, 8318-8323. 2000 National Academy of Science, U.S.A.

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