Systematic searches

The availability of complete genomes/proteomes makes it possible to search systematically for the combination of amino acid residues, which is most important for protein themostability (41, 54). An exhaustive enumeration of all possible subsets of 20 amino acids is performed by representing sets of amino acids by vectors, where each component at of the vector takes the value of 1 if the amino acid of type i is presented in the set and 0 otherwise. Thus, 2 - 2 = 524,286 linearly independent nontrivial combinations exist. Given fP, the fraction of amino... 

Deterministic search Systematic scanning of the potential energy surface, that is, generation of starting geometries by systematic variation of internal coordinates followed by structure optimization (see Potential energy surface and Conformational search). 

Rainer Herges has developed algorithms to search systematically for new reactions. With the computer system IGOR, he and his co-workers have predicted hitherto unknown reactions and realised them in the laboratory. 

Soon after Becquerel s discovery of uranium s radioactivity, Marie Sklodowska Curie (1867—1934), also working in France, studied the radioactivity of thorium (Th) and began to search systematically for new radioactive elements. She showed that the radioactivity of uranium was an atomic property— that is, its radioactivity was proportional to the amount of the element present and was not related to any particular compound. Her experiments indicated that other radioactive elements were probably also present in certain uranium samples. With painstaking technique, she and her husband Pierre Curie (1859-1906) separated the element radium (Ra) from uranium ore and found that it is more than one million times more radioactive than uranium. In 1903, Marie and Pierre Curie shared the Nobel Prize in physics with Henri Becquerel for their discovery of radioactivity. After Pierre died. 

Inspection must be an active and creative search process, of developing hypotheses about how the system might go wrong. It requires the allocation of time and mental resources. Checklists can help to make the search systematic and to avoid forgetting things, but they should not be allowed to become a substitute for active thinking. 

Most text-searching systems permit a variety of textsearching methods. This section will suggest how some of these commonly available methods can be applied to searching systematic nomenclature. 

Unfortunately the matrix whose elements appear in (8.4.9) is usually rather large and solution by inversion is not convenient. There are various ways of avoiding direct solution of (8.4.9). The simplest is to assume that is approximately diagonal, with elements E . The equations (8.4.9) are then uncoupled and A = —(all rs)- Since each element A defines a 2 x 2 rotation, this approximation is equivalent to defining an optimum rotation for each pair rs and then performing all rotations simultaneously, as if they were independent. This is reminiscent of the methods introduced by Hinze and others (Section 8.3) but here the second-order terms are admitted in a more satisfactory way and the aim is to search systematically for the stationary point rather than to satisfy the stationary-value conditions. 

By means of the performance measure H x) described above, systematic and iterative search for good parameter values can be performed. In this work, one systematic and two iterative search methods were explored. 

In this section, the systematic search for conical intersections based on the Longuet-Higgins phase-change rule is described. For conciseness sake, we limit the present discussion to Hiickel-type systems only, unless specifically noted otherwise. The first step in the antilysis is the determination of the LH loops containing a conical intersection for the reaction of interest. 

A given pair of anchors may be part of several loops, containing different conical intersections. A systematic search for the third anchor is conducted by considering the electrons that are to be re-paired (i.e., that form the chemical bonds that are created in the reaction), A pragmatic and systematic way of doing this is by considering first the re-pairing of the smallest possible number of... 

A molecular dynamics simulation samples the phase space of a molecule (defined by the position of the atoms and their velocities) by integrating Newton s equations of motion. Because MD accounts for thermal motion, the molecules simulated may possess enough thermal energy to overcome potential barriers, which makes the technique suitable in principle for conformational analysis of especially large molecules. In the case of small molecules, other techniques such as systematic, random. Genetic Algorithm-based, or Monte Carlo searches may be better suited for effectively sampling conformational space. 

Woodruff and co-workers introduced the expert system PAIRS [67], a program that is able to analyze IR spectra in the same manner as a spectroscopist would. Chalmers and co-workers [68] used an approach for automated interpretation of Fourier Transform Raman spectra of complex polymers. Andreev and Argirov developed the expert system EXPIRS [69] for the interpretation of IR spectra. EXPIRS provides a hierarchical organization of the characteristic groups that are recognized by peak detection in discrete ames. Penchev et al. [70] recently introduced a computer system that performs searches in spectral libraries and systematic analysis of mixture spectra. It is able to classify IR spectra with the aid of linear discriminant analysis, artificial neural networks, and the method of fe-nearest neighbors. 

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