Molecular Dynamics 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... 

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 ... 

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). 

The United States is currently a leader in most areas of theoretical/ computational chemistry. In basic theory, Europe has many talented young investigators. Within the next 10 years, given these demographics, the U.S. leadership will be challenged by Europe in electronic structure and basic theory development. This trend does not characterize the entire field of theoretical chemistry. For example, Monte Carlo and molecular dynamics simulation methods were invented in the United States, and to this day, the United States maintains a strong position, especially in quantum Monte Carlo calculations. 

Molecular dynamic simulation methods, in addition to being essential for interpreting NMR data at the atomic level, also augment experimental studies in a number of other ways [101] modeling techniques can (i) yield structural information where experimental data has not yet been acquired, (ii) expand on experimental data through simulations that yield dynamic trajectories whose analysis provides unique information on lesion mobility, and (iii) provide thermodynamic insights by ensemble analysis using statistical mechanical methods. Furthermore, reaction mechanisms can now be determined with some confidence by combined quantum mechanical and molecular mechanical methods [104, 105],... 

Pak Y, Wang S. Application of a molecular dynamics simulation method with a generalized effective potential to the flexible molecular docking problems. J Phys Chem B 2000 104 354-359. 

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