On the methods of construction and evaluation of reaction coordinates from direct dynamics
Abstract/Contents
- Abstract
- With the emerging interest in using non-linear dimensionality reduction (NLDR) methods to study and generate meaningful reaction coordinates for complex dynamical systems, it is important not only to find methods most suited for these types of data but to have methods of evaluating the quality of these different mappings. Methods that perform well for lower energy, simpler ground state reactions are not necessarily suitable for describing the reaction path of more complex ground state reactions or high energy excited state reactions. NLDR is a good candidate for finding reaction coordinates for excited such systems where assumptions used to generate reaction coordinates for ground state reactions do not hold. In this dissertation we explore how different data featurizations and NLDR methods affect the mapping quality of excited state dynamics simulation of ethylene and RPSB analogue. We also introduce techniques to determine the quality of these mappings using several existing, general techniques for comparing the different NLDR mappings and by adapting those general techniques to specifically evaluate the mappings of molecular dynamics simulation data. Having a metric to compare the quality of different NLDR mapping allows us to approach the construction of reaction coordinates in a systematic way.
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 | 2019; ©2019 |
| Publication date | 2019; 2019 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Author | Izmailov, Sofia |
|---|---|
| Degree supervisor | Martinez, Todd J. (Todd Joseph), 1968- |
| Thesis advisor | Martinez, Todd J. (Todd Joseph), 1968- |
| Thesis advisor | Markland, Thomas E |
| Thesis advisor | Zare, Richard N |
| Degree committee member | Markland, Thomas E |
| Degree committee member | Zare, Richard N |
| Associated with | Stanford University, Department of Chemistry. |
Subjects
| Genre | Theses |
|---|---|
| Genre | Text |
Bibliographic information
| Statement of responsibility | Sofia Izmailov. |
|---|---|
| Note | Submitted to the Department of Chemistry. |
| Thesis | Thesis Ph.D. Stanford University 2019. |
| Location | electronic resource |
Access conditions
- Copyright
- © 2019 by Sofia Izmailov
- License
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
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