Please use this identifier to cite or link to this item: http://hdl.handle.net/11023/2156
Title: Nonadiabatic Control for Quantum Information Processing and Biological Electron Transfer
Author: Babcock, Nathan S.
Advisor: Sanders, Barry C.
Salahub, Dennis R.
Keywords: Biology--Molecular;Biochemistry;Physics--Atomic
Issue Date: 23-Apr-2015
Abstract: In this Thesis, I investigate two disparate topics in the fields of quantum information processing and macromolecular biochemistry, inter-related by the underlying physics of nonadiabatic electronic transitions (i.e., the breakdown of the Born-Oppenheimer approximation). The main body of the Thesis is divided into two Parts. In Part I, I describe my proposal for a two-qubit quantum logic gate to be implemented based on qubits stored using the total orbital angular momentum states of ultracold neutral atoms. I carry out numerical analyses to evaluate gate fidelity over a range of gate speeds, and I derive a simple criterion to ensure adiabatic gate operation. I propose a scheme to significantly improve the gate's fidelity without decreasing its speed. I contribute to the development of a “loophole-free” Bell inequality test based on the use of this gate by carrying out an order-of-magnitude feasibility analysis to assess whether the test is viable given realistic technological limitations. In Part II, I investigate electron transfer reaction experiments performed on native and mutant forms of the MADH--amicyanin redox complex derived from P. denitrificans. I implement molecular dynamics simulations of native and mutant forms of the solvated MADH--amicyanin complex. I analyze the resulting nuclear coordinate trajectories, both geometrically and in terms of electronic redox coupling. I find that the interprotein solvent dynamics of the mutant systems differ dramatically from those of the native system, and that the stability of an electron-transfer-mediating ``water bridge'' is compromised in the mutant complexes. I conclude that the mutations disrupt a protective “molecular breakwater” on the surface of amicyanin that stabilizes the interprotein water bridge. I discuss parallels between the nonadiabatic effects as they manifest themselves in the two systems, and I suggest how my findings in Part I promote technological developments to better characterize systems like that examined in Part II.
URI: http://hdl.handle.net/11023/2156
Appears in Collections:Electronic Theses

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