Computer simulation methodology

Studied both by computer simulation and by experiment. Throughout this chapter we will assume that the reader has a basic understanding of computer simulation methodology and liquid state theory. We also point out that for publishing convenience all figures have been collected in the centre of this chapter. 

Here we consider various aspects of statistical mechanics (see also chapter A2.3 and [2,1]) that have a direct bearing on computer simulation methodology. 

The treatment of counterions around DNA in computer simulations requires a thorough knowledge of several aspects of this problem, including the structure of DNA, computer simulation methodology, electrostatic interactions,and analysis techniques. " Detailed discussions of all these topics are beyond the scope of this chapter. However, we provide brief overviews of these... 

There is a variety of computer simulation methodologies that have been applied to study the properties of grafted polymer layers. They include Monte-Carlo (MC) simulations, Molecular Dynamics (MD) simulations, and Brownian Dynamics (BD) simulations. These methodologies have been applied on a variety of model systems, including lattice chains, off-lattice chains, and Edwards Hamiltonians. A recent excellent review of the application of simulation methods has been written by Grest and Murat. Here we just discuss the applicability of the simulations methods in general, their advantages and limitations. 

The finiteness of molecular systems, the geometric nature of the structural transitions, and the constraints (e.g., stiff bonds) that affect the mechanical motion render a theoretical treatment typically very difficult. For this reason, computer simulations and efficient algorithms are inevitable tools that help unravel the properties of structural transitions of molecular systems. We will discuss various examples throughout this book, where efficient computer simulation methodologies were employed to obtain the statistical information needed for a thermodynamic analysis of such transitions. Therefore, a short review of... 

Despite the enormous success of the zeolite membrane, practical application in a larger scale is still limited. Several factors such as cost of membrane development, reproducibility, long-term stability, and the method for the preparation of the defect-free membrane restrict its implementation in the industry. Molecular simulations become a powerful tool to predict the catalytic behavior of zeolite [14]. Compared to the experimental process, it is rapid and convenient, is cost effective, can handle more complex systems within a reasonable period of time, and results to better understanding of the system. Many computer simulation methodologies have been employed to understand the physicochemical properties of zeolite such as adsorption characteristics [15], diffusion and permeation [16], catalytic reaction [17], and also the nature of the acidic site [18,19]. The main concern of this work is to design a membrane using computer simulation methodology. 

Computer simulations in general, and MD in particular, represent a new scientific methodology. Theoretical breakthroughs involve both new concepts and the mathematical tools of development. 

Gunsteren W F and H J C Berendsen 1990. Computer Simulation of Molecular Dynamics Methodology, Applications and Perspectives in Chemistry. Angewandte Chemie International Edition in English 29 992-1023. 

See van Gunsteren, W.F. Berendsen, H.J.C. Computer simulation of molecular dynamics-methodology, applications, and perspectives in chemistry Angewandre Chemie, International Edition in English, 29 992-1023, 1990, and Karplus, M. Petsko, G.A. Molecular dynamics simulations in biology Nature 347 631-639, 1990. 

On several occasions, the reader will notice a direct connection between the topics covered in the book and other, related areas of statistical mechanics, such as the methodology of computer simulations, nonequilibrium dynamics or chemical kinetics. This is hardly a surprise because free energy calculations are at the nexus of statistical mechanics of condensed phases. 

Van Gunsteren WF Berendsen HJC. Computer simulation of molecular dynamics methodology, application and perspectives in chemistry. Angew. Chem. Int. Ed. Eng. 1990 29 992-996. 

Peter Kusalik took up an appointment at Dalhousie University in 1989 and developed a research program focused on computer simulation studies of molecular liquids, solids, and solutions. As well as standard simulation approaches, he has explored nonequilibrium molecular dynamics techniques and applied field simulations, the development of new models and methodologies being one aim of his research. A common focus throughout his work has been the examination of the interplay between microscopic structure and dynamics in condensed matter and their relationship to bulk properties. 

The need for computer simulations introduces some constraints in the description of solvent-solvent interactions. A simulation performed with due care requires millions of moves in the Monte Carlo method or an equivalent number of time steps of elementary trajectories in Molecular Dynamics, and each move or step requires a new calculation of the solvent-solvent interactions. Considerations of computer time are necessary, because methodological efforts on the calculation of solvation energies are motivated by the need to have reliable information on this property for a very large number of molecules of different sizes, and the application of methods cannot be limited to a few benchmark examples. There are essentially two different strategies. 

This chapter will not review all of the published studies, but instead will focus on examples of computer simulations of phospholipid membrane systems ranging from simple models through descriptions of lipid and water in full atomic detail to complex membranes containing small solutes, lipids, and proteins. The chapter is aimed at medicinal chemists who are interested in drug-phospholipid interactions. Before discussing the results of different simulations, the currently applied methodologies will briefly be described. 

Table 8.1 describes the steps of the methodology in more detail. The procedure starts with the Problem definition production rate, chemistry, product specifications, safety, health and environmental constraints, physical properties, available technologies. Then, a first evaluation of feasibility is performed by an equilibrium design. This is based on a thermodynamic analysis that includes simultaneous chemical and physical equilibrium (CPE). The investigation can be done directly by computer simulation, or in a more systematic way by building a residue curve map (RCM), as explained in the Appendix A. This step will identify additional thermodynamic experiments necessary to consolidate the design decisions, mainly phase-equilibrium measurements. Limitations set by chemical equilibrium or by thermodynamic boundaries should be analyzed here. 

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