Reptation sequencing

When the method was applied to one-component and two-component"" melts of polypropylene chains of specific stereochemical sequence, reptation was included along with the single-bead moves, in order to achieve equilibration of the melts on an acceptable time scale. The polypropylenes (especially syndiotactic polypropylene) equilibrate slowly if the simulation uses single bead moves only. 

The efficiency of a MC algorithm depends on the elementary moves it employs to go from one configuration to the next in the sequence. An attempted move typically involves changing a small number of degrees of freedom it is accepted or rejected according to selection criteria designed so that the sequence ultimately conforms to the probability distribution of interest. In addition to usual moves of molecule translation and rotation practiced for small-molecule fluids, special moves have been invented for polymers. The reptation (slithering... 

The sequence of pores followed by a polyelectrolyte chain (DNA, de-naturated protein, etc.) is called the tube [148], whereas the section of chain contained in one pore (of typical size a), is called a blob [119, 149]. Escape from the tube along the chain contour can occur only by loops or hernias (Fig. 19b), in which each pore of the gel is crossed by the chain twice instead of once. In the absence of electric field, De Gennes has shown that such events are exponentially unprobable due to an associated entropy loss of order kT per blob escaped [149] Macroscopic diffiision occurs by a reptation motion in which... 

The simulations in Ref. 22 were performed using the UA approximation (see above) with the methods and the force field already described. The same 6-12 potential was used for the mutual interactions of the methyl and methylene groups and for their interactions with the atomic units comprising the solid surfaces. A total of 1297 tridecane molecules was introduced in the basic cell one at a time in such a way that two nonbonded units (including those of the solid surfaces) could not come within 0.32 run from each other. The system was then equilibrated at 300 K using the reptation technique. The results shown in the next sections represent the average over 10 different equilibrium models obtained in sequence and separated by more than 800000 accepted reptations. It was verified that the tridecane molecules were able to diffuse during the simulation from the narrow slits to the wider slits and vice versa. 

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