Theoretical advances toward understanding recent experiments in biophysical chemistry

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.

Department dc:contributor.department

Massachusetts Institute of Technology. Dept. of Chemistry.

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2012

Author dc:creator

• Zimanyi, Eric Norman

Advisor dc:contributor.advisor

• Jianshu Cao and Robert J. Silbey.

• Chemistry.

Statement dc:rights

• 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.

Licence dc:rights.uri

• http://dspace.mit.edu/handle/1721.1/7582

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/1721.1/73181

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/73181