Extracting Equilibrium From Nonequilibrium: Free Energy Calculation From Steered Molecular Dynamics Simulations
Park, Sanghyun
This item is only available for download by members of the University of Illinois community. Students, faculty, and staff at the U of I may log in with your NetID and password to view the item. If you are trying to access an Illinois-restricted dissertation or thesis, you can request a copy through your library's Inter-Library Loan office or purchase a copy directly from ProQuest.
Permalink
https://hdl.handle.net/2142/80500
Description
Title
Extracting Equilibrium From Nonequilibrium: Free Energy Calculation From Steered Molecular Dynamics Simulations
Author(s)
Park, Sanghyun
Issue Date
2004
Doctoral Committee Chair(s)
Schulten, Klaus
Department of Study
Physics
Discipline
Physics
Degree Granting Institution
University of Illinois at Urbana-Champaign
Degree Name
Ph.D.
Degree Level
Dissertation
Keyword(s)
Physics, Condensed Matter
Language
eng
Abstract
This thesis explores the issue of calculating potentials of mean force (an equilibrium property) from steered molecular dynamics simulations (a nonequilibrium process). Recently discovered Jarzynski's equality provides the theoretical basis. Derivations of Jarzynski's equality are reviewed and related theoretical issues are discussed. A method of potential-of-mean-force calculation is developed; the method is based on the cumulant expansion of Jarzynski's equality and the scheme of using stiff springs for the purpose of steering. The possibility that the resulting work distribution might be Gaussian regardless of the speed of the process is discussed. A benchmark study using deca-alanine as an exemplary system examines the accuracy of the method and demonstrates the Gaussian nature of the work distribution. The method is then applied to a process involving an actual protein, glycerol conduction through the membrane channel protein GlpF. From the potential of mean force thus obtained, important observables such as the binding constant and conductivity are estimated. And finally, the problem of finding reaction paths is discussed: a new method based on mean first-passage times is proposed and is applied to the excitation migration in photosynthesis.
Use this login method if you
don't
have an
@illinois.edu
email address.
(Oops, I do have one)
IDEALS migrated to a new platform on June 23, 2022. If you created
your account prior to this date, you will have to reset your password
using the forgot-password link below.
