Regional overlap techniques

If the two important regions do not overlap, or overlap only partially, it is usually necessary to use the enhanced sampling techniques introduced in Sect. 1.4. This is schematically illustrated in Fig. 2.4d. One of these techniques, stratification, has... 

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)...

As the initial and final states are set by the problem under study, their important phase space relationship could be any one of the cases illustrated in Fig. 6.1. For cases Fig. 6.1c, d, it is impossible to construct a funnel path from 0 to 1 directly. To satisfy the funnel requirement, similar to the MFEP calculation, a staged NEW calculation can be performed. For example, in the case Fig. 6.1c, one can first construct an intermediate in the common region of / ,[ and /), then perform two separate NEW calculations following the paths 0 —> M and 1 —> M, respectively. This NEW-overlap sampling (NEW-OS) technique will be discussed in detail in Sect. 6.6. 

It would be valuable if one could proceed with a reliable free energy calculation without having to be too concerned about the important phase space and entropy of the systems of interest, and to analyze the perturbation distribution functions. The OS technique [35, 43, 44, 54] has been developed for this purpose. Since this is developed from Bennett s acceptance ratio method, this will also be reviewed in this section. That is, we focus on the situation in which the two systems of interest (or intermediates in between) have partial overlap in their important phase space regions. The partial overlap relationship should represent the situation found in a wide range of real problems. 

The intense Texas Red fluorophore has a QY that is inherently higher than the tetrameth-ylrhodamine or Lissamine rhodamine B derivatives. Texas Red s luminescence is shifted maximally into the red region of the spectrum, and its emission peak only minimally overlaps with that of fluorescein. This makes Texas Red derivatives among the best choices of labels for use in double-staining techniques. 

The main objective of the Workshop was to bring together people working in areas of Fundamental physics relating to Quantum Field Theory, Finite Temperature Field theory and their applications to problems in particle physics, phase transitions and overlap regions with the areas of Quantum Chaos. The other important area is related to aspects of Non-Linear Dynamics which has been considered with the topic of chaology. The applications of such techniques are to mesoscopic systems, nanostructures, quantum information, particle physics and cosmology. All this forms a very rich area to review critically and then find aspects that still need careful consideration with possible new developments to find appropriate solutions. 

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