Algorithms and Computer Implementation

The determination of the ETSA is the main goal of the ET method. With the ETSA known, one can easily work our methods of 

Nonexperimental computer screening of new molecules with respect to the activity. 

The computational scheme for the ET method includes the following stages for the series of compounds under investigation  

Calculation of atomic and bonding electronic parameters [atomic charges, bond orders, polarizabilities, HOMO (LUMO) energies, etc.]. 

The possibilities of dividing the molecule into fragments are limited by at 

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Martello, S., and Toth, P. (1990), Knapsack Problems Algorithms and Computer Implementations, John Wiley Sons, New York. 

All automatic procedures and more recent methods " generate feasible chemical structures from groups by relying primarily on the valence of groups. Examples of groups of valence 1, 2, and 3 are shown in Table I. Some methods take a symbolic and qualitative approach in constructing compounds while others adopt a quantitative optimization-oriented approach. We will keep our discussion away from such algorithmic and computer implementation details, so that it encompasses both types of techniques. 

Once again, specific algorithms and computer programs have not been included. The wide range of mathematical software now available makes implementation relatively simple and the reader is encouraged to experiment and play with their data to appreciate and understand the techniques and treatments discussed. It is even more important now than at the time of publication of the first edition that analysts and spectroscopists have an understanding of the basics of chemometrics. 

The ultimate vision of computational chemistry is to provide a virtual laboratory for chemical explorations. The goal is not to replace but rather complement the real lab. In the virtual lab, it is easy to change experimental conditions and to experiment with hypothetical what-if scenarios. Virtual synthesis of chemical compoimds can be done with a few mouse-clicks, whereas the virtual measurement of physical and chemical properties is the often burdensome task of a computational engine based on the laws of classical and/or quantum physics. Most research efforts, therefore, are aimed at improving the algorithms and approximations implemented in the computational engines. The main role of quantum chemical response theory, which is the subject of this chapter, is the virtual measmement of optical properties of molecules. 

In the next few chapters, we present computer simulations as a natural extension of statistical mechanical theories. We detail the methodological steps and provide a clear sequence of numerical steps, algorithms and computer codes to implement Monte Carlo and molecular dynamics simulations of simple systems. The reader will also benefit from numerous program codes made freely available on this book s sourceforge project at http //sourceforge.net/projects/statthermo. In this chapter we discuss prereqvusite steps in all computer simulations. 

We have implemented several edge and region segmentation algorithms and image enhancement techniques on an IBM personnel computer, in C++ language. 

This completes the outline of FAMUSAMM. The algorithm has been implemented in the MD simulation program EGO VIII [48] in a sequential and a parallelized version the latter has been implemented and tested on a number of distributed memory parallel computers, e.g., IBM SP2, Cray T3E, Parsytec CC and ethernet-linked workstation clusters running PVM or MPI. 

A NSS has a computational implementation we have called a GNDL [1,4]. The Fortran code of the algorithm implementing a GNDL can be found described in Program 1 below. The GNDL algorithm constitutes the link between the mathematical notation of the NSS and the computer codification of this operator. 

Most of the algorithms and formulae discussed in this chapter can be implemented as expressions in computer spreadsheets, and the rest as simple computer programs. Most are also incorporated into the Microsoft Excel spreadsheet program by the Isoplot add-in (Ludwig 1999, in press) as user-available functions and graphical routines (Appendix III). 

Typical examples such as the ones mentioned above, are used throughout this book and they cover most of the applications chemical engineers are faced with. In addition to the problem definition, the mathematical development and the numerical results, the implementation of each algorithm is presented in detail and computer listings of selected problems are given in the attached CD. 

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