Computational geometry techniques

J., Zheng, W. (2008) Novel approach to structure-based pharmacophore search using computational geometry and shape matching techniques. / Chem Inf Model 48, 889-901. 

In terms of computing adiabatic energy differences, if the Bom-Oppenheimer PES for the excited state can be computed, geometry optimization of that state may be carried out using standard techniques. But, as we have been discussing above, we have not yet devised a scheme for computing the excited-state surface, since ground-state orbitals are not appropriate for minimum-determinantal excited-state wave functions. How then to obtain a better excited-state wave function ... 

The reader, then, should be able to acquire the basic theory and a fair idea of the kinds of results to be obtained from the common computational chemistry techniques. You will learn how one can calculate the geometry of a molecule, its IR and UV spectra and its thermodynamic and kinetic stability, and other information needed to make a plausible guess at its chemistry. 

As discussed in Chapter 1, the full three-dimensional structure of a compound can be optimized with almost any of the quantum computational techniques. Since most quantum chemical computations are still performed on a single molecule in the gas phase, these computed structures can be most readily compared to gas-phase experimental structures. In the following chapters, we will present a number of case studies where computed and experimental geometries are compared. To get a sense of the quality of computed geometries, a few selected cases are discussed next. 

The processes in real corroding systems are obviously more complicated than represented by this model. Useful quantitative calculation of the distribution of current density, and hence corrosion rate along the surface, based on the polarization curves for the anodic and cathodic reactions and on the geometry of the anodic and cathodic sites is very complex. In principle, computer-based techniques can be used if exact polarization curves and the geometry of the anodic and cathodic areas are available. For most industrially important situations, this information is not available. Also, time-dependent factors, such as film formation, make quantitative calculations of long-time corrosion rates very uncertain. The theory underlying these calculations, however, has been useful in interpreting observations in research and in industrial situations. 

Luo T, Papa DA, Li Z, Sze CN, Alpert CJ, Pan DZ (2008) Pyramids an efficient computational geometry-based approach for timing-driven placement. In ICCAD, pp 204-211 Shi W, Li Z, Alpert CJ (2004) Complexity analysis and speedup techniques for optimal buffer insertion with minimum cost. In ASP-DAC, pp 609-614... 

Dividing computational geometry into primitive shapes is needed to solve the conservation equations explained in Section 6.2 for each mesh element. The number of elements in a computational mesh and chosen numerical technique to solve conservation equations determines the accuracy of a computational model. If the computational mesh consists of many mesh elements, the computational... 

In this paper we report on the first results of a calculation by Monte Carlo computer-simulation techniques of the mass transport coefficient in a lattice gas model. We calculate in a rectangular geometry the mass flux, Q(T), and the mass density profile, p(x, r), for an open system which is subject to an externally imposed chemical potential gradient, x is a spatial coordinate. From these quantities, the mass transport coefficient, D(T), can be derived using the equivalent of Ohm s law. 

This paper describes the development of a novel system for improving the quality of information provided by manual ultrasonic examination of welds, while retaining the flexibility of the human operator to apply the techniques to components of a wide range of geometries and dimensions. The system, known as CamuS (Computer Aided Manual UltraSonics) provides assistance to the manual operator in two separate areas ... 

Baker J 1993 Techniques for geometry optimization a comparison of Cartesian and natural Internal coordinates J. Comput. Chem. 14 1085... 

---