The Orthogonal Space Tempering Scheme and Its Application to Complex Biomolecular Processes

• Other Authors: Harris, William T. (William Thomas) (authoraut)
• Format: Others
• Language: English; English
• Published: Florida State University
• Subjects: Chemistry; Biophysics
• Online Access: http://purl.flvc.org/fsu/fd/FSU_2015fall_Harris_fsu_0071E_12913

Molecular dynamics (MD) simulations have advanced greatly in the recent decades, but are not without their limitations. This work first details the pitfalls of MD simulations, then presents the details of a new, robust method, orthogonal space tempering (OST) which can achieve accurate and efficient sampling in MD simulations as well as accurate recovery of desired thermodynamic quantities. This method is then applied to understanding the mechanistic details and free energy of passive transmembrane permeation of small molecules through a lipid bilayer, as well as bulky and charged species. Furthermore, the method is applied to the study of the conformational and dynamical properties of a very important human neuropeptide Y homologue, avian pancreatic peptide. === A Dissertation submitted to the Department of Chemistry & Biochemistry in partial fulfillment of the Doctor of Philosophy. === Fall Semester 2015. === November 12, 2015. === Includes bibliographical references. === Wei Yang, Professor Directing Dissertation; Per-Arne Rikvold, University Representative; Ken Knappenberger, Committee Member; Oliver Steinbock, Committee Member.