Theoretical advances toward understanding recent experiments in biophysical chemistry
Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2012.
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| Format: | Thesis |
| Language: | eng |
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Massachusetts Institute of Technology
2012
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| Online Access: | http://hdl.handle.net/1721.1/73181 |
| _version_ | 1811092935026933760 |
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| author | Zimanyi, Eric Norman |
| author2 | Jianshu Cao and Robert J. Silbey. |
| author_facet | Jianshu Cao and Robert J. Silbey. Zimanyi, Eric Norman |
| author_sort | Zimanyi, Eric Norman |
| collection | MIT |
| description | Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2012. |
| first_indexed | 2024-09-23T15:36:01Z |
| format | Thesis |
| id | mit-1721.1/73181 |
| institution | Massachusetts Institute of Technology |
| language | eng |
| last_indexed | 2024-09-23T15:36:01Z |
| publishDate | 2012 |
| publisher | Massachusetts Institute of Technology |
| record_format | dspace |
| spelling | mit-1721.1/731812019-04-12T20:21:43Z Theoretical advances toward understanding recent experiments in biophysical chemistry Zimanyi, Eric Norman Jianshu Cao and Robert J. Silbey. Massachusetts Institute of Technology. Dept. of Chemistry. Massachusetts Institute of Technology. Dept. of Chemistry. Chemistry. Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2012. This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. Cataloged from student-submitted PDF version of thesis. Includes bibliographical references. Several theoretical advances are presented, with the common theme of helping better understand and guide recent experiments in biophysical chemistry. In Chapter 2, I consider a recent criticism of the Jarzynski equality, notably that a breakdown in the connection between work and changes in the Hamiltonian for time-dependent systems causes the Jarzynski equality to produce unphysical results. I discuss the relationship between two possible definitions of free energy and demonstrate that it is indeed possible to obtain physically relevant free energy profiles from the Jarzynski equality, thereby resolving the recent questions in the literature. Next, I consider several aspects of coherent resonance energy transfer. In Chapter 3, I present a theory for coherent resonance energy transfer based on classical electrodynamics and demonstrate how it is able to capture dynamics in the coherent regime, the incoherent regime, and in between these two limits. In Chapter 4, I present a quantum theory for resonant energy transfer based on using a variational polaron transform to optimally split the Hamiltonian into a zeroth-order part and a perturbation. I then apply a quantum master equation to obtain the dynamics of energy transfer for various parameters. Finally, in Chapter 5, I examine whether it is possible to use the known exact equilibrium state of the system to improve the variational procedure. by Eric Norman Zimanyi. Ph.D. 2012-09-26T14:18:14Z 2012-09-26T14:18:14Z 2012 2012 Thesis http://hdl.handle.net/1721.1/73181 809794840 eng M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission. http://dspace.mit.edu/handle/1721.1/7582 119, [2] p. application/pdf Massachusetts Institute of Technology |
| spellingShingle | Chemistry. Zimanyi, Eric Norman Theoretical advances toward understanding recent experiments in biophysical chemistry |
| title | Theoretical advances toward understanding recent experiments in biophysical chemistry |
| title_full | Theoretical advances toward understanding recent experiments in biophysical chemistry |
| title_fullStr | Theoretical advances toward understanding recent experiments in biophysical chemistry |
| title_full_unstemmed | Theoretical advances toward understanding recent experiments in biophysical chemistry |
| title_short | Theoretical advances toward understanding recent experiments in biophysical chemistry |
| title_sort | theoretical advances toward understanding recent experiments in biophysical chemistry |
| topic | Chemistry. |
| url | http://hdl.handle.net/1721.1/73181 |
| work_keys_str_mv | AT zimanyiericnorman theoreticaladvancestowardunderstandingrecentexperimentsinbiophysicalchemistry |