Space topology

Shakhnovich BE, Deeds E, Delisi C, Shakhnovich E. Protein structure and evolutionary history determine sequence space topology. Genome Res. 2005 15 385-392. 

The use of fractal and percolation concepts to characterize pore-space topology (Sahimi, 1993) is a notable exception. 

In materials of infinite extent, the above definitions remain valid. As noted previously (Chapter 4), for pore space topologies with a given coordination number, there exists a critical filling probability (porosity). In materials with filling probabilities above this critical value, the size of the largest cluster is comparable to the size of the lattice. The presence of this lattice spanning cluster does not require that the material be finite in extent in fact, most analytical results in percolation theory assume that the lattice is infinite. For... 

Figure 3 Common node space topology after PDG placement for the auto-correlation with N = 512 and P — 50.

Frisch determines IPNs as topologically interpenetrating systems. According to Irzhak [25] the topological structure of a polymer is determined by the connectivity of the structural elements, and may be described as a graph independent of the real chemical and spatial structure and disposition of its elements in space. Topological knots are labile formations that reveal them-... 

First, a few definitions a system is any region of space, any amount of material for which the boundaries are clearly specified. At least for thennodynamic purposes it must be of macroscopic size and have a topological integrity. It may not be only part of the matter in a given region, e.g. all the sucrose in an aqueous solution. A system could consist of two non-contiguous parts, but such a specification would rarely be usefLil. 

SmA phases, and SmA and SmC phases, meet tlie line of discontinuous transitions between tire N and SmC phase. The latter transition is first order due to fluctuations of SmC order, which are continuously degenerate, being concentrated on two rings in reciprocal space ratlier tlian two points in tire case of tire N-SmA transition [18,19 and 20], Because tire NAC point corresponds to the meeting of lines of continuous and discontinuous transitions it is an example of a Lifshitz point (a precise definition of tliis critical point is provided in [18,19 and 20]). The NAC point and associated transitions between tire tliree phases are described by tire Chen-Lubensky model [97], which is able to account for tire topology of tire experimental phase diagram. In tire vicinity of tire NAC point, universal behaviour is predicted and observed experimentally [20]. 

In this section, the adiabatic picture will be extended to include the non-adiabatic terais that couple the states. After this has been done, a diabatic picture will be developed that enables the basic topology of the coupled surfaces to be investigated. Of particular interest are the intersection regions, which may form what are called conical intersections. These are a multimode phenomena, that is, they do not occur in ID systems, and the name comes from their shape— in a special 2D space it has the fomi of a double cone. Finally, a model Flamiltonian will be introduced that can describe the coupled surfaces. This enables a global description of the surfaces, and gives both insight and predictive power to the fomration of conical intersections. More detailed review on conical intersections and their properties can be found in [1,14,65,176-178]. 

Figure 6. Two-dimensional (top) and 3D (bottom) representations of a peaked (a) and sloped (b) conical intersection topology. There are two directions that lift the degeneracy the GD and the DC. The top figures have energy plotted against the DC while the bottom figures represent the energy plotted in the space of hoth the GD and DC vectors. At a peaked intersection, as shown at the bottom of (a), the probability of recrossing the conical intersection should be small whereas in the case of a sloped intersection [bottom of ( )l, this possibility should be high. [Reproduced from [84] courtesy of Elsevier Publishers.]...

One of the main outcomes of the analysis so far is that the topological matrix D, presented in Eq. (38), is identical to an adiabatic-to-diabatic transformation matrix calculated at the end point of a closed contour. From Eq. (38), it is noticed that D does not depend on any particular point along the contour but on the contour itself. Since the integration is carried out over the non-adiabatic coupling matrix, x, and since D has to be a diagonal matrix with numbers of norm 1 for any contour in configuration space, these two facts impose severe restrictions on the non-adiabatic coupling terms. 

The general formula and the individual cases as presented in Eq. (97) indicate that indeed the number of conical intersections in a given snb-space and the number of possible sign flips within this sub-sub-Hilbert space are interrelated, similar to a spin J with respect to its magnetic components Mj. In other words, each decoupled sub-space is now characterized by a spin quantum number J that connects between the number of conical intersections in this system and the topological effects which characterize it. 

In Section IV, we introduced the topological matrix D [see Eq. (38)] and showed that for a sub-Hilbert space this matrix is diagonal with (-1-1) and (—1) terms a feature that was defined as quantization of the non-adiabatic coupling matrix. If the present three-state system forms a sub-Hilbert space the resulting D matrix has to be a diagonal matrix as just mentioned. From Eq. (38) it is noticed that the D matrix is calculated along contours, F, that surround conical intersections. Our task in this section is to calculate the D matrix and we do this, again, for circular contours. 

If compounds have the same topology (constitution) but different topography (geometry), they are called stereoisomers. The configuration expresses the different positions of atoms around stereocenters, stereoaxes, and stereoplanes in 3D space, e.g., chiral structures (enantiomers, diastereomers, atropisomers, helicenes, etc.), or cisftrans (Z/E) configuration. If it is possible to interconvert stereoisomers by a rotation around a C-C single bond, they are called conformers. 

Topological descriptors and 3D descriptors calculated in distance space", such as 3D autocorrelation, surface autocorrelation, and radial distribution function... 

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