Structural ordering maps

Although the bond-orientational metrics defined above have proven useful for identifying numerous space-filling crystalline morphologies43 like face-centered cubic, body-centered cubic, simple cubic, and hexagonally close-packed lattices, they are inadequate for detecting order in systems that organize 

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The conditions on the phase diagram for which this anomalous behavior occurs has been termed water s structurally anomalous region. Inspection of the order map (Figure 4) reveals a dome of structural anomalies within the temperature-density plane, bounded by loci of maximum tetrahedral order (at low densities) and minimum translational order (at high densities) as shown in Figure 5. Also marked on Figure 5 are regions of diffusive anomalies,... 

Continuing with the mini-theme of computational materials chemistry is Chapter 3 by Professor Thomas M. Truskett and coworkers. As in the previous chapters, the authors quickly frame the problem in terms of mapping atomic (chemical) to macroscopic (physical) properties. The authors then focus our attention on condensed media phenomena, specifically those in glasses and liquids. In this chapter, three properties receive attention—structural order, free volume, and entropy. Order, whether it is in a man-made material or found in nature, may be considered by many as something that is easy to spot, but difficult to quantify yet quantifying order is indeed what Professor Truskett and his coauthors describe. Different types of order are presented, as are various metrics used for their quantification, all the while maintaining theoretical rigor but not at the expense of readability. The authors follow this section of their... 

Thus as we go across the isoelectronic series Ge - GaAs -> ZnSe - CuBr, the degree of ionicity increases from 0 -> 0.32 -> 0.56 - 0.71 as expected. A noteable achievement of the Phillips-Van Vechten ionicity scale was that it also allowed an excellent structural ordering of the sp-valent octet compounds. As shown in Fig. 3.4, the structure map ( c, E ) separates all those... 

Like the retina, the visual cortex is a layered structure, in v hich different cell groups perform different tasks. Along its tv o-dimensional surface, one finds an orderly mapped representation of the outside world. Unlike the retina, the cortex consists of multiple areas, hierarchically organized, each of which performs a partial processing task in the analysis of the scene around us. At the present time, over 30 visual cortical areas per hemisphere are recognized in monkey, and a smaller number of more expanded areas are thought to exist in humans. 

For example, C could be the category of topological spaces, or abstract simplicial complexes, or posets, in which case the structure-preserving maps would respectively be continuous maps, or simplicial maps, or order-preserving maps (see Definition 10.3). 

The above discussion is consistent with the possible existence of two well-defined classes of liquids simple and water like. The formers interact via spherically symmetric nonsoftened potentials and do not exhibit thermodynamic or dynamic anomalies. One can calculate translational and orientational order parameters t and ( ), and project equilibrium state points onto the (f, q) plane thereby generating what is termed the Errington Debenedetti (ED) order map [24]. In water like liquids, interactions are orientation dependent these liquids exhibit dynamic and thermodynamic anomalies, and their ED order map is in general two dimensional but becomes linear (or quasi linear) when the liquid exhibits structural, dynamic, or thermodynamic anomalies. 

The fourth summation corresponds to an energy function for all atoms j not directly bonded to atom /, and represented by a van der Waals attractive and repulsive energy term. This term is essential for nucleic acid model building in order to maintain a reasonable base stacking such that the stacked base planes are approximately parallel and separated by about 3.4 A. In addition to this, the fourth summation is used to constrain certain specified pairs of atoms at hydrogen bond distances. Thus, we initially specified in the refinement the base-paired secondary structure as well as the tertiary structure hydrogen bonds which could be seen in the MIR and partial group structure Fourier maps. 

Tama et al. developed in the past years a protocol called molecular dynamics-flexible fitting In this proeedure, the normal modes of a protein of known structure are eomputed using simple elastic network model approaches (as described in Seetion 3.2). Then, the protein scaffold is deformed along the computed normal modes in order to fit the electron density map coming from an EM experiment. Once the structure of the protein that best fit the experimental data is found, the atomistic-detailed structure is mapped back starting from the original high-resolution data. In this way, the different conformations of a protein present in a Cryo-EM data set can be resolved at atomistic resolution. 

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