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**1 - 6**of**6**### Molecular Dynamics and Stochastic Simulations of Surface Diffusion

, 2007

"... Despite numerous advances in experimental methodologies capable of addressing the various phenomenon occurring on metal surfaces, atomic scale resolution of the microscopic dynamics remains elusive for most systems. Computational models of the processes may serve as an alternative tool to fill this ..."

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Despite numerous advances in experimental methodologies capable of addressing the various phenomenon occurring on metal surfaces, atomic scale resolution of the microscopic dynamics remains elusive for most systems. Computational models of the processes may serve as an alternative tool to fill this void. To this end, parallel molecular dynamics simulations of self-diffusion on metal surfaces have been developed and employed to address microscopic details of the system. However these simulations are not without their limitations and prove to be computationally impractical for a variety of chemically relevant systems, particularly for diffusive events occurring in the low temperature regime. To circumvent this difficulty, a corresponding coarse-grained representation of the surface is also developed resulting in a reduction of the required computational effort by several orders of magnitude, and this description becomes all the more advantageous with increasing system size and complexity. This representation provides a convenient framework to address fundamental aspects of diffusion in nonequilibrium environments and an interesting mechanism for directing diffusive motion along the surface is explored. In the ensuing discussion, additional topics including transition state theory in noisy systems and the construction of a checking function for protein structure validation are outlined. For decades the former has served as a cornerstone for estimates of chemical reaction rates. However, in complex environments transition state theory most always provides only an upper bound for the true rate. An alternative approach is described that may alleviate some of the difficulties associated with this problem. Finally, one of the grand challenges facing the computational sciences is to develop methods capable of reconstructing protein structure based solely on readily-available sequence information. Herein a checking function is developed that may prove useful for addressing whether a particular proposed structure is a viable possibility.

### Transition state theory in liquids beyond planar dividing surfaces

"... The success of Transition State Theory (TST) in describing the rates of chemical reactions has been less-than-perfect in solution (and sometimes even in the gas phase) because conventional dividing surfaces are only approximately free of recrossings between reactants and products. Recent advances in ..."

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The success of Transition State Theory (TST) in describing the rates of chemical reactions has been less-than-perfect in solution (and sometimes even in the gas phase) because conventional dividing surfaces are only approximately free of recrossings between reactants and products. Recent advances in dynamical systems theory have helped to identify the interconnected manifolds —“superhighways” — leading from reactants to products. The existence of these manifolds has been proven rigorously, and explicit algorithms are available for their calculation. We now show that these extended structures can be used to obtain reaction rates directly in dissipative systems. We also suggest a treatment for the substantially more general case in which the molecular solvent is fully specified by the positions of all its atoms. Specifically, we can construct effective solvent configurations for which the exact TST manifolds can be constructed and used to sample the rates of an open system.

### Escape Rates and its Application to Systems of Ferromagnets

, 2008

"... This Theses, Ph.D is brought to you for free and open access by the Science at ..."

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This Theses, Ph.D is brought to you for free and open access by the Science at