Cluster displacements

MacNeil, T., Gewain, K. M., and MacNeil, D. J. (1993). Deletion analysis of the avermectin biosynthetic genes of Streptomyces avermitilis by gene cluster displacement. J. Bacteriol. 175, 2552-2563. 

FeS cluster displacement experiments on Cp2 in 80% hexamethylphos-phoramide, Tris buffer + thiophenol yielded spectra very similar to those obtained by extruding clusters from C. pasteurianum ferredoxin (4Fe4S clusters) and quite dissimilar to that with bovine adrenodoxin which contains a 2Fe2S cluster (Orme-Johnson et ai, 1977). 

In Chap. 4 we left induction after the proof of the Frobenius reciprocity theorem. In that proof the important concept of the positional representation was introduced. This described the permutation of the sites under the action of the group elements. Further, we defined local functions on the sites which transformed as irreps of the site symmetry. As an example, if we want to describe the displacement of a cluster atom in a polyhedron, two local functions are required a totally-symmetric one for the radial displacement and a twofold-degenerate one for the tangential displacements. In cylindrical symmetry, these are labelled a and tt, respectively. The mechanical representation, i.e. the representation of the cluster displacements, is then the sum of the two induced representations ... 

Fig. 18 a Macroion acceptance ratio and b macroion root-mean-square displacement per MC pass as a function of the cluster displacement parameter for System 11 from simulations with cluster trial moves using pd = 1.0 and indicated cluster radii R i in Ru units. At = Rm fhe single-particle move is recovered. In a, the acceptance ratio equal to 0.5, and in b, the relation = A /i/2 are given (dotted lines). Nm = 20 and Npass = 10 ... 

Features of the cluster displacement approach are further illustrated in Fig. 19, displaying acceptance ratio, macroion rms displacement, and mun-ber of cluster members as a function of the electrostatic coupUng parameter Tii at Zr = 80 using the cluster displacement parameter d = Ru at different cluster radii Rc. At an electrostatic coupling below Tn 0.03, cluster trial moves are sHghtly iirferior to single-macroion trial moves (smaller acceptance ratio and smaller see Fig. 19a and b, respectively). As the... 

Finally, the present comparison has been made for salt-free systems. It should be mentioned that the performance of single-macroion trial moves is essentially salt independent, whereas the performance of cluster trial moves deteriorates upon addition of salt, making the difference in their performances smaller. Nevertheless, the cluster displacement procedure is advantageous up to considerable salt concentrations. A promising method to improve... 

Fig. 21 Snapshots showing the equilibration from an initially homogeneous and unstable configuration where the second level of cluster displacement is used. Nu = 20 and the snapshots are separated by Wpass = 5 x 10 passes. = 40, < m = 0.01, and Fn = 1.940...

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