Zeolites to peptides: Statistical mechanics methods for structure solution and property evaluation
Pophale, Ramdas S.
Deem, Michael W.
Doctor of Philosophy
Methods in statistical mechanics are used to study structure and properties of zeolites and peptides. A Monte Carlo method is applied to solve structure of a newly synthesized zeolite. Understanding the structure of a zeolite could lead to optimization of chemical processes it is involved in. Dielectric constant and elastic modulus are calculated using a molecular dynamics method for a pure silica zeolite with and without the structure directing agent used in its synthesis. These properties are of interest due to the potential use of this zeolite as low dielectric constant material in manufacturing integrated circuits. Results of four methods probing energy landscapes in peptides are compared for four cyclic peptides. Their ability to equilibrate structural properties and their relative speeds are important in their ability to simulate complex structures. A docking study is carried out to probe interactions between two proteins, Cripto and Snail, and E-cadherin promoter. The study supports experimental evidence that Cripto is involved in expression of E-cadherin through a promoter priming mechanism. Finally, the use of computational models in the design of better vaccines is illustrated through an example of Influenza.
Engineering; Materials science