Canonical correspondence

Faye, B., Lescourret, F., Dorr, N., Tillard, E., MacDermott, B. and McDermott, J., (1997a), Interrelationships between herd management practices and udder health status using canonical correspondence analysis . Preventive Veterinary Medicine, 32, 171-192. 

Figure 6. Canonical correspondence analysis for surface sediments of 41 lakes in British Columbia, Canada, that encompass a broad range of trophic states. Circles represent lakes and triangles represent the 25 most abundant diatom taxa. Arrows indicate environmental variables that correlate most strongly with the distribution of diatom taxa and lake-water chemistry, as detected by forward selection. Maximum depth (Zntax) and total phosphorus (TP) were transformed by using the In (x + 1) function. This analysis is discussed in detail in reference 46.

Figure 8. Normalized components of the first two eigenvectors of the Canonical Correspondence Analysis, showing the relative contributions from the 31 leaf characteristics. The order of the characteristics corresponds to that in Tables 4 and 5. Within each eigenvector, the components are normalized by the maximum value which are respectively, 1.08 and 0.88. [Used by permission of Geological Society of America, from Forest et al. (1999), Geol. Soc. Am. Bull., Vol. Ill, Fig. 11, p. 509.]...

Stull R (1989) An Introduction to Boundary Layer Meteorology. Kluwer Academic Publ. ter Braak CJF (1986) Canonical correspondence analysis A new eigenvector technique for multivariate direct gradient analysis. Ecology 67 1167-1179... 

Detrended Canonical Correspondence Analysis (ter Braak and Smilauer, 2002) was used successively to compare the macroinvertebrate communities at the three... 

The canonical ensemble is a set of systems each having the same number of molecules N, the same volume V and the same temperature T. This corresponds to putting the systems in a thennostatic bath or, since the number of systems is essentially infinite, simply separating them by diathennic walls and letting them equilibrate. In such an ensemble, the probability of finding the system in a particular quantum state / is proportional to where UfN, V) is tire energy of the /th quantum state and /c, as before, is the Boltzmaim... 

The grand canonical ensemble is a set of systems each with the same volume V, the same temperature T and the same chemical potential p (or if there is more than one substance present, the same set of p. s). This corresponds to a set of systems separated by diathennic and penneable walls and allowed to equilibrate. In classical thennodynamics, the appropriate fimction for fixed p, V, and Tis the productpV(see equation (A2.1.3 7)1 and statistical mechanics relates pV directly to the grand canonical partition function... 

Consider two systems in thennal contact as discussed above. Let the system II (with volume and particles N ) correspond to a reservoir R which is much larger than the system I (with volume F and particles N) of interest. In order to find the canonical ensemble distribution one needs to obtain the probability that the system I is in a specific microstate v which has an energy E, . When the system is in this microstate, the reservoir will have the energy E = Ej.- E due to the constraint that the total energy of the isolated composite system H-II is fixed and denoted by Ej, but the reservoir can be in any one of the R( r possible states that the mechanics within the reservoir dictates. Given that the microstate of the system of... 

The canonical distribution corresponds to the probability density for the system to be in a specific microstate with energy E- H, from it one can also obtain the probability P( ) that the system has an energy between E and E + AE i the density of states D E) is known. This is because, classically. 

The canonical ensemble corresponds to a system of fixed and V, able to exchange energy with a thennal bath at temperature T, which represents the effects of the surroundings. The thennodynamic potential is the Helmholtz free energy, and it is related to the partition fiinction follows ... 

Since H=K. + V, the canonical ensemble partition fiinction factorizes into ideal gas and excess parts, and as a consequence most averages of interest may be split into corresponding ideal and excess components, which sum to give the total. In MC simulations, we frequently calculate just the excess or configurational parts in this case, y consists just of the atomic coordinates, not the momenta, and the appropriate expressions are obtained from equation b3.3.2 by replacing fby the potential energy V. The ideal gas contributions are usually easily calculated from exact... 

The grand canonical ensemble corresponds to a system whose number of particles and energy can fluctuate, in exchange with its surroundings at specified p VT. The relevant themiodynamic quantity is the grand potential n = A - p A. The configurational distribution is conveniently written... 

In a dense system, the acceptance rate of particle creation and deletion moves will decrease, and the number of attempts must be correspondingly increased eventually, there will come a point at which grand canonical simulations are not practicable, without some tricks to enliance the sampling. 

This coordinate transformation gives rise to a corresponding transformation of the momenta via the canonical lift transformation [10]. Thus the corresponding conjugate momenta are p R, defined by... 

In this expression. Ait is the size of the integration time step, Xj is a characteristic relaxation time, and T is the instantaneous temperature. In the simulation of water, they found a relaxation time of Xj = 0.4 ps to be appropriate. However, this method does not correspond exactly to the canonical ensemble. 

In our last example we return to the issue of the possible damaging effects of the standard geometry constraints. Two long trajectories have been computed for a partially hydrated dodecamer DNA duplex of the previous example, first by using ICMD and second with Cartesian coordinate molecular dynamics without constraints [54]. Both trajectories started from the same initial conformation with RMSD of 2.6 A from the canonical B-DNA form. Figure 5 shows the time evolution of RMSD from the canonical A and B conformations. Each point in the figure corresponds to a 15 ps interval and shows an average RMSD value. We see that both trajectories approach the canonical B-DNA, while the RMSD... 

It is clear that Eq. (85) is numerically reliable provided is sufficiently small. However, a detailed investigation in Ref. 69 reveals that can be as large as some ten percent of the diameter of a fluid molecule. Likewise, rj should not be smaller than, say, the distance at which the radial pair correlation function has its first minimum (corresponding to the nearest-neighbor shell). Under these conditions, and if combined with a neighbor list technique, savings in computer time of up to 40% over conventional implementations are measured for the first (canonical) step of the algorithm detailed in Sec. IIIB. These are achieved because, for pairwise interactions, only 1+ 2 contributions need to be computed here before i is moved U and F2), and only contributions need to be evaluated after i is displaced... 

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