Torsion dynamics

Updating a Torsional Dynamic Tester for Fourier Transform Rheometry.825... 

FIGURE 30.6 Updating a closed cavity torsional dynamic tester for Fourier transform (FT) rheometry. 

J.L. Leblanc and A. Mongmel, A thorough examination of a commercial torsional dynamic rheometer with a closed oscillating cavity, Prog. Rubber Plast. TechnoL, 17, 162-185, 2001. 

J.L. Leblanc and C. de la Chapelle, Updating a torsional dynamic rheometer for Fourier transform rheometry on mbber materials. Rubber Chem. TechnoL, 76, 287-298, 2003. 

Nucleic acids flexibility torsion dynamics helix structure deformation due to intercalating agents photocleavage accessibility carcinogenesis... 

It is conceivable that diffusion of kinks, or overdamped solitons, along the DNA could act to relax the FPA with a time dependence similar to that predicted for torsional deformation/31 32) High levels of intercalated dyes would be expected to alter both the equilibrium population of kinks and their mobility along the DNA. Hence, this question is addressed by examining the effect of intercalating dyes on the torsional dynamics. 

An ethanol-condensed aggregate manifests FPA relaxation and X-ray diffraction results similar to those obtained for the viruses with nonglucosylated DNAs, albeit with even more restricted motion.(57) The interhelix spacing in the ethanol-induced aggregate was similar to that of the X, XA, and T4dC DNAs (2.7 nm), but shorter than that in spermidine-induced aggregates (3.0nm), which showed relatively normal torsional dynamics.(57)... 

P.-G. Wu, L. Song, J. B. Clendenning, B. S. Fujimoto, A. S. Benight, and J. M. Schurr, Interaction of chloroquine with linear and supercoiled DNAs. Effect on the torsional dynamics, rigidity, and twist energy parameter, Biochemistry 27, 8128-8144 (1988). 

Thomas, J. C., Allison, S. A., Appellof, C. J., and Schurr, J. M. (1980). Torsion dynamics and depolarization of fluorescence of linear macromolecules. II. Fluorescence polarization anisotropy measurements of a clean viral phi 29 DNA. Biophys. Chem. 12, 177-188. 

In this example of model reactive polymer processing of two immiscible blend components, as with Example 11.1, we have three characteristic process times tD,, and the time to increase the interfacial area, all affecting the RME results. This example of stacked miscible layers is appealing because of the simple and direct connection between the interfacial layer and the stress required to stretch the multilayer sample. In Example 11.1 the initially segregated samples do create with time at 270°C an interfacial layer around each PET particulate, but the torsional dynamic steady deformation torques can not be simply related to the thickness of the interfacial layer, <5/. However, the initially segregated morphology of the powder samples of Example 11.1 are more representative of real particulate blend reaction systems. 

Figure 8 The impact of hot-spot residue pair conformations on contact formation during docking of barnase (bn) and barstar (bs). Contact formation (as measured by the percentage of native contacts) during the first 100 ps of torsion dynamics simulations is shown see text for details.

The results of simulating barnase-barstar association after 100 ps of simple multiple copy MD without ensemble enriching are shown in Figure 9. Whereas contact formation in the simple multiple copy MD simulation has leveled off after the initial 100 ps, ensemble enriching with a linear scoring function is able to shift the ensemble population toward a higher number of established native contacts. Compared to the side-chain torsion dynamics... 

Fig. 3.3 Internal energy and number of hopping residues along a reproducible representative FM trajectory for the thermophilic variant of protein G. A hopping residue is defined as tagged for a Ramachandran basin transition in the coarse-grained stochastic process that underlies the FM torsional dynamics. Reprinted from [35], with permission from Elsevier...

In chemistry studies, we have measured fluorescence decay of phthalazine in various solvents (21). depolarization decay times of rhoda-mine 6G in various solvents (22), and torsional dynamics of DNA (23). 

Fluorescence depolarization anisotropy of ethidium bromide bound to DNA has been used to examine the torsion dynamics of this linear macromolecule. 

H. W. Schranz and M. A. Collins,/. Chem. Phys., 98, 1132 (1993). Nonlinear Resonance and Torsional Dynamics Model Simulations of HOOH and CH3OOCH3. H. W. Schranz and M. A. Collins, /. Chem. Phys., 101,307 (1994). A Model Classical Study of Nonlinear Resonance and Torsional Isomerization. 

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