Dynamical simulation methods

The Monte Carlo and molecular dynamics simulation methods can be used to explor the conformational space of molecules. During such a simulation the system is able t... 

Good reviews of the application of dynamic simulation methods to biomolecules can be found in the books by Brooks et al. [1] and McCammon and Harvey [2]. Good short reviews on this topic can also be found in Refs. 3-5. More detailed discussions of dynamic simulation methodologies can be found in books by Allen and Tildesley [6], Frenkel and Smit [7], and Rapaport [8] and in the review by van Gunsteren [9]. 

Thermodynamic properties. A molecular-dynamics simulation method (using a steepest decent method) with Stillinger-Weber potential is employed to optimize structures and to obtain the cohesive en-... 

In contrast to the single molecule case, Monte Carlo methods tend to be rather less efficient than molecular dynamics in sampling phase space for a bulk fluid. Consequently, most of the bulk simulations of liquid crystals described in Sect. 5.1 use molecular dynamics simulation methods. 

Tomoo, K., Matsushita, Y., Fujisaki, H., Abiko, F., Shen, X., Taniguchi, T., Miyagawa, H., Kitamura, K., Miura, K., and Ishida, T. (2005). Structural basis for mRNA cap-binding regulation of eukaryotic initiation factor 4E by 4E-binding protein, studied by spectroscopic, X-ray crystal structural, and molecular dynamics simulation methods. Biochim. Biophys. Acta 1753, 191—208. 

Hofer, T. S. Randolf, B. R. Rode, . M. In Challenges and Advances in Computational Chemistry and Physicsvol. 6 Ed. Canute, S. Molecular Dynamics Simulation Methods Including Quantum Effects. Springer Heidelberg, 2008. 

Ray Kapral came to Toronto from the United States in 1969. His research interests center on theories of rate processes both in systems close to equilibrium, where the goal is the development of a microscopic theory of condensed phase reaction rates,89 and in systems far from chemical equilibrium, where descriptions of the complex spatial and temporal reactive dynamics that these systems exhibit have been developed.90 He and his collaborators have carried out research on the dynamics of phase transitions and critical phenomena, the dynamics of colloidal suspensions, the kinetic theory of chemical reactions in liquids, nonequilibrium statistical mechanics of liquids and mode coupling theory, mechanisms for the onset of chaos in nonlinear dynamical systems, the stochastic theory of chemical rate processes, studies of pattern formation in chemically reacting systems, and the development of molecular dynamics simulation methods for activated chemical rate processes. His recent research activities center on the theory of quantum and classical rate processes in the condensed phase91 and in clusters, and studies of chemical waves and patterns in reacting systems at both the macroscopic and mesoscopic levels. 

MOLECULAR DYNAMICS SIMULATION METHODS INCLUDING QUANTUM EFFECTS... 

In this chapter we will mostly focus on the application of molecular dynamics simulation technique to understand solvation process in polymers. The organization of this chapter is as follow. In the first few sections the thermodynamics and statistical mechanics of solvation are introduced. In this regards, Flory s theory of polymer solutions has been compared with the classical solution methods for interpretation of experimental data. Very dilute solution of gases in polymers and the methods of calculation of chemical potentials, and hence calculation of Henry s law constants and sorption isotherms of gases in polymers are discussed in Section 11.6.1. The solution of polymers in solvents, solvent effect on equilibrium and dynamics of polymer-size change in solutions, and the solvation structures are described, with the main emphasis on molecular dynamics simulation method to obtain understanding of solvation of nonpolar polymers in nonpolar solvents and that of polar polymers in polar solvents, in Section 11.6.2. Finally, the dynamics of solvation with a short review of the experimental, theoretical, and simulation methods are explained in Section 11.7. 

Describe the basic principles of the Monte Carlo and molecular dynamic simulation methods applied to electrolytes. How are the adjustable parameters determined ... 

In this section, we will briefly describe the static and dynamic simulation methods and then give some results for the liquid of greatest geochemical importance water. Applications of such methods to mineral structures will be discussed in later chapters. 

As mentioned earlier many two-phase gas-liquid flows are highly dynamic and this property requires the use of dynamic simulation methods. A well-known example of such a type of flow is encountered in bubble columns where recirculating flow structures are present which are not stationary but which continuously change their size and location in the column. Due to their frequent application in chemical reaction engineering and their relatively simple geometry, CFD analyses of bubble columns have received significant attention and are discussed in more detail here. 

Molecular dynamics simulation methods are currently the most popular approaches. This method is for the analysis of protein flexibility and dynamic properties of molecular systems. With respect to docking, these simulations could provide a realistic view of the docking process, however, these calculations are still out of reach. Therefore, dynamical simulations during the docking process are limited to the protein-ligand complexes. Molecular dynamical simulations are often... 

On the other hand, it is not the goal of this book to present an exhaustive review of the measurement of physico-chemical properties carried out in the last two or three decades. This would certainly exceed the framework of this book. The electrochemistry of molten salts is not included in this book either, since in my opinion, this topic would need a separate book due to its complexity and wealth of applications. The quantum chemistry and molecular dynamics simulation methods are omitted as well. 

J. M. Haile and S. Gupta, Extensions of the molecular dynamics simulation method 2. Isothermal systems. J. Chem. Phys. 79, 3067 (1983). 

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