Overlapping ensembles

This means that particle configurations where at least two particles overlap, i.e., have a distance r smaller than the diameter cr, are forbidden. They are forbidden because the Boltzmann factor contains a term, exp(—oo) 0, that leads to a vanishing statistical weight. Hence we have an ensemble of... 

Fig. 2.4. Schematic representation of the different relationships between the important regions in phase space for the reference (0) and the target (1) systems, and their possible interpretation in terms of probability distributions - it should be clarified that because AU can be distributed in a number of different ways, there is no obvious one-to-one relation between P0(AU), or Pi (AU), and the actual level of overlap of the ensembles [14]. (a) The two important regions do not overlap, (b) The important region of the target system is a subset of the important region of the reference system, (c) The important region of the reference system overlaps with only a part of the important region of the target state. Then enhanced sampling techniques of stratification or importance sampling that require the introduction of an intermediate ensemble should be employed (d)...

This approach is one of the oldest techniques for improving FEP calculations [36]. It is often called the simple overlap sampling (SOS) method and is usually markedly more accurate than simple averaging. It requires that one forward and one backward calculation be performed at every intermediate state. It is worth noting that no sampling is performed from the ensemble characterized by Xi+AX/2, so that the number of stages is the same as in the pure forward, or backward calculation. 

Since the bias function should enhance the sampling of pathways with important work values it can be made to depend on the work only, ir[z 2 ) = n W( (. Z))]. To minimize the statistical error in the free energy difference the bias function needs to be selected such that both the statistical errors of the numerator and the denominator of (7.44) are small. Ideally, the bias function should have a large overlap with both the unbiased work distribution P(W) and the integrand of (7.36), P (W) exp (—j3W). Just as Sun s work-biased ensemble Pa[z( ), the biased path ensemble )] can... 

In the canonical example, we could estimate the free energy difference between two runs by examining the overlap in their probability distributions. Similarly, in the grand canonical ensemble, we can estimate the pressure difference between the two runs. If the conditions for run I arc f//1. V. > ) and for run 2 (po, VjK), then... 

Hogenesch, J.B., et al., "A Comparison of the Celera and Ensembl Predicted Gene Sets Reveals Little Overlap in Novel Genes," Cell, 106, 413-415 (2001). 

An interesting application of these principles is the prediction of CO dissociation routes on the closed-packed (111) surface of rhodium (see Fig. A.17). Two factors determine how the dissociation of a single CO molecule proceeds. First, the geometry of the final situation must be energetically more favorable than that of the initial one. This condition excludes final configurations with the C and the O atom on adjacent Rh atoms, because this would lead to serious repulsion between the C and O atoms. A favorable situation is the one sketched in Fig. A.17, where initially CO occupies a threefold hollow site, and after dissociation C and O are in opposite threefold sites. The second requirement for rupture of the CO molecule is that the C-0 bond is effectively weakened by the interaction with the metal. This is achieved when the C-O bond stretches across the central Rh atom. In this case there is optimum overlap between the d-electrons of Rh in orbitals, which extend vertically above the surface, and the empty antibonding orbitals of the CO molecule. Hence, the dissociation of CO requires a so-called catalytic ensemble of at least 5 Rh atoms [8,21,22]. 

To understand this effect, one can imagine an overlap integral (see Fig. 2) as a composition of overlap integrals formed by individual donor-acceptor pairs in an inhomogeneous ensemble of dye molecules. As explained in Sect. 5.1, at... 

As mentioned in Sec. 1.3, the electrochemical potential of electrons in condensed phases corresponds to the Fermi level of electrons in the phases. There are two possible cases of electron ensembles in condensed phases one to which the band model is applicable (in the state of degenera< where the wave functions of electrons overlap), and the other to which the band model cannot apply (in the state of nondegeneracy where no overlap of electron wave functions occurs). In the former case electrons or holes are allowed to move in the bands, while in the latter case electrons are assumed to be individual particles rather than waves and move in accord with a thermal hopping mechanism between the a4jacent sites of localized electron levels. 

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