Improving and applying atomistic simulation to study biophysical conformational dynamics
Abstract/Contents
- Abstract
- Models are tools used to interpret and draw conclusions from nature. Molecular dynamics (MD) simulation is a powerful technique for modeling complex atomistic systems such as biomolecules. In this dissertation, I discuss how one can improve and apply MD simulation in order to learn about biophysical phenomena. I first discuss how to improve the representation of the underlying physical interactions in a simulation. Chapter 2 discusses the optimization method, and 3 discusses how to rigorously characterize a resultant potential function. I then discuss how to use Markov state modeling to derive an interpretable mechanistic characterization of a simulation dataset. Chapters 4 and 5 apply this framework to study the conformational dynamics of the TREK-2 and CLC-2 ion channels, respectively. A brief introduction to the topics of MD simulation, force field optimization, and Markov state modeling is given in chapter 1. There remains a lot of work to be done before simulations are able to mimic reality with high fidelity. However, I am optimistic that with increasing data availability and improvements in optimization methodology, simulation will prove itself progressively more useful for studying dynamics at atomic resolution.
Description
| Type of resource | text |
|---|---|
| Form | electronic resource; remote; computer; online resource |
| Extent | 1 online resource. |
| Place | California |
| Place | [Stanford, California] |
| Publisher | [Stanford University] |
| Copyright date | ©2018 |
| Publication date | 2018; 2018 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Author | McKiernan, Keri A |
|---|---|
| Degree supervisor | Maduke, Merritt C, 1966- |
| Degree supervisor | Pande, Vijay |
| Thesis advisor | Maduke, Merritt C, 1966- |
| Thesis advisor | Pande, Vijay |
| Thesis advisor | Markland, Thomas E |
| Thesis advisor | Martinez, Todd J. (Todd Joseph), 1968- |
| Degree committee member | Markland, Thomas E |
| Degree committee member | Martinez, Todd J. (Todd Joseph), 1968- |
| Associated with | Stanford University, Department of Chemistry. |
Subjects
| Genre | Theses |
|---|---|
| Genre | Text |
Bibliographic information
| Statement of responsibility | Keri A. McKiernan. |
|---|---|
| Note | Submitted to the Department of Chemistry. |
| Thesis | Thesis Ph.D. Stanford University 2018. |
| Location | electronic resource |
Access conditions
- Copyright
- © 2018 by Keri Ann McKiernan
- License
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
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