Jumping between wells

The solid phase presents some fundamental differences from liquid and gas phases. First, the effect the solid has on the electronic structure of a sorbate can be profound (e.g., H2 chemidissociation on metals). Thus new processes may be energetically accessible in solid-state systems that are not important in liquid or gas phases. Second, dynamical processes in solid-state systems can be significantly different from those in liquid or gas phases. The average environment that a solute molecule encounters in gas and liquid phases is translationally invariant. This is not true for the solid with well-defined lattice sites e.g., the average environment a solute molecule sees near a lattice site is very different from that near an interstitial site. Therefore, diffusion of sorbates in or on a solid can often be treated as isolated jumps between well-defined sorption sites, and the diffusion constant can be approximated from the rate constants for isolated jumps. 

Figure 8 shows a one-dimensional sketch of a small fraction of that energy landscape (bold line) including one conformational substate (minimum) as well as, to the right, one out of the typically huge number of barriers separating this local minimum from other ones. Keeping this picture in mind the conformational dynamics of a protein can be characterized as jumps between these local minima. At the MD time scale below nanoseconds only very low barriers can be overcome, so that the studied protein remains in or close to its initial conformational substate and no predictions of slower conformational transitions can be made. 

L.133 Using two sets of backbone RDC data, collected in bacteriophage Pfl and bicelle media, they obtained order tensor parameters using a set of crystallographic coordinates for the structural model. This allowed the refinement of C -C bond orientations, which then provided the basis for their quantitative interpretation of C -H RDCs for 38 out of a possible 49 residues in the context of three different models. The three models were (A) a static xi rotameric state (B) gaussian fluctuations about a mean xi torsion and (C) the population of multiple rotameric states. They found that nearly 75% of xi torsions examined could be adequately accounted for by a static model. By contrast, the data for 11 residues were much better fit when jumps between rotamers were permitted (model C). The authors note that relatively small harmonic fluctuations (model B) about the mean rotameric state produces only small effects on measured RDCs. This is supported by their observation that, except for one case, the static model reproduced the data as well as the gaussian fluctuation model. 

So far we only considered transport of particles by diffusion. As mentioned in 1 the continuous description was not strictly necessary, because diffusion can be described as jumps between cells and therefore incorporated in the multivariate master equation. Now consider particles that move freely and should therefore be described by their velocity v as well as by their position r. The cells A are six-dimensional cells in the one-particle phase space. As long as no reaction occurs v is constant but r changes continuously. As a result the probability distribution varies in a way which cannot be described as a succession of jumps but only in terms of a differential operator. Hence the continuous description is indispensable, but the method of compounding moments can again be used. 

Model. A difference equation for the material balance was obtained from a discrete reactor model which was devised by dividing the annulus into a two dimensional array of cells, each taken to be a well stirred batch reactor. The model supposes that axial motion of the mobile phase and bed rotation occur by instantaneous discontinuous jumps, between cells. Reaction occurs only on the solid surface, and for the reaction type A B + C used in this work, -dn /dt = K n - n n. Linear isotherms, n = BiC, were used, and while dispersion was not explicitly included, it could be simulated by adjusting the number of cells. The balance is given by Eq. 2, where subscript n is the cell index in the axial direction, and subscript m is the index in the circumferential direction. 

It is interesting to note that, for malonic acid (which is structurally related to DMMA), the activation energy measured from XH NMR Tx measurements [170] is 5.6 kj mol-1, which is significantly lower than in DMMA and is assigned to proton jumps between the two minima of an asymmetric double well potential. This emphasises the importance of the effect of the crystal packing on the asymmetry of the potential function, which defines the mechanism of the proton dynamics in carboxylic acid dimers. 

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