Exploring the Solvent Environment of Biomolecular Systems.

protein solvation and hydration;implicit solvent model refactoring;refactoring for CUDA and parallel processing;mapping preferential solvation;slowdown of solvent dynamics over extended distances;ph modeling through lambda dynamics;Chemistry;Science;Chemistry

Arthur, Evan J.Geva, Eitan ;

University of Michigan

关键词: protein solvation and hydration;    implicit solvent model refactoring;    refactoring for CUDA and parallel processing;    mapping preferential solvation;    slowdown of solvent dynamics over extended distances;    ph modeling through lambda dynamics;    Chemistry;    Science;    Chemistry;   

Others  :  https://deepblue.lib.umich.edu/bitstream/handle/2027.42/116689/evanarth_1.pdf?sequence=1&isAllowed=y

瑞士|英语

来源: The Illinois Digital Environment for Access to Learning and Scholarship

【 摘 要 】

Solvent interactions at the protein-solvent interface facilitate many biological processes such as protein-protein recognition, protein-DNA binding, and a variety of enzymatic mechanisms. Consequently, developing a comprehensive understanding of solvation effects has been pursued for many decades, and promises benefits to many branches of biomolecular science. The following series of studies explore the maturation and improvement of several computational solvent models and analytical methods for studying protein-solvent interactions, and is divided into two principle sections. In the first half we create a detailed analysis of the protein-solvent interface, and explore dynamic mechanisms proteins employ for structural stability. The second half we follow the development and refactoring of accurate implicit solvent models to take advantage of modern parallel processing chips, and in doing so we enable new timescales for studying conformational equilibria and titration states.