Doctor of Philosophy (PhD)
We have applied our new approach, a combination of the AVUS-HR nucleation algorithm and a thermodynamic cycle, to the studies of hydrophobicity-related researches. Due to the multifaceted characteristics of hydrophobicity, it is essential to acquire knowledge in various environments where hydrophobic relevant events occur for comprehensive understanding of this process. In this regards, we have chosen two relatively unstudied hydrophobic subjects for application of our new methodology. For the first subject, hydrophobic association behaviors of a methane pair confined into a nanometer sized hydrophobic cavity have been investigated. Our new approach demonstrates that the association behavior between two methane molecules is enhanced under confined environment rather than in bulk water. This association is primarily driven by energy originating from the unique situation where small (i.e., two methane molecules) and large (i.e., boundary of the hydrophobic cavity) hydrophobic units come together. For the second subject, hydration thermodynamics for confined spaces between two infinitely parallel walls have been studied. Our simulation results demonstrate that the weak attractive interaction between water molecules and walls allows water molecules to pack more efficiently for the smallest wall separation of 3 Å considered here comparing with the hard wall case where there is no interaction between water molecules and walls. Furthermore, these weak attractive interactions lower the free energy penalty for the formation of water clusters inside a confined space, ultimately lowering the total energy of the system when compared with the hard wall. Based on the successful applications of our novel nucleation algorithm to the two different hydrophobic related researches, further, we believe that it will contribute to the various and more complex hydrophobic researches (i.e., association behaviors of nonpolar and/or polar amino acid residues in the presence of salts under confined environment, and effects of salts, temperature and pressure on this association behaviors) as well as nucleation studies under confined environment.
Document Availability at the Time of Submission
Secure the entire work for patent and/or proprietary purposes for a period of one year. Student has submitted appropriate documentation which states: During this period the copyright owner also agrees not to exercise her/his ownership rights, including public use in works, without prior authorization from LSU. At the end of the one year period, either we or LSU may request an automatic extension for one additional year. At the end of the one year secure period (or its extension, if such is requested), the work will be released for access worldwide.
Kim, Hyunmi, "A Multifaceted Phenomenon of Hydrophobic Effects: Insights Learned from Nucleation Algorithm Based Computer Simulation Approach" (2011). LSU Doctoral Dissertations. 48.