Geometries, from various experimental methods

They compared the PME method with equivalent simulations based on a 9 A residue-based cutoflF and found that for PME the averaged RMS deviations of the nonhydrogen atoms from the X-ray structure were considerably smaller than in the non-PME case. Also, the atomic fluctuations calculated from the PME dynamics simulation were in close agreement with those derived from the crystallographic temperature factors. In the case of DNA, which is highly charged, the application of PME electrostatics leads to more stable dynamics trajectories with geometries closer to experimental data [30]. A theoretical and numerical comparison of various particle mesh routines has been published by Desemo and Holm [31]. 

With the supposition that the slip layer is thin and the slip velocity is constant, various analyses have been developed in the search for the ideal experimental method to define slip. The Mooney analysis (20) for both tube flow and concentric cylinder flow has been applied to a wide range of materials including polymer solutions (21), filled suspensions (22), semisolid foods (23), fruit purees (24), and ketchups (25). Alternate estimates of slip velocity have been determined experimentally from, parallel plate torsion flow (26), from flow data in channels and inclined planes, and from porous medium geometries (8). 

All these formulas are approximations in that various edge and end effects have been neglected, as well as states of strain and flow which may be somewhat more complicated than the simple forms assumed from the geometry. In some cases, better approximations have been introduced for specific experimental methods. The possible effect of surface tension on the mechanical measurements is usually not considered, but may be important if there is a change in surface area with the mechanical deformation. 

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