Sanders, Barry C.Salahub, Dennis R.Babcock, Nathan S.2015-04-232015-06-222015-04-232015Babcock, N. S. (2015). Nonadiabatic Control for Quantum Information Processing and Biological Electron Transfer (Doctoral thesis, University of Calgary, Calgary, Canada). Retrieved from https://prism.ucalgary.ca. doi:10.11575/PRISM/27114http://hdl.handle.net/11023/2156In 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.engUniversity of Calgary graduate students retain copyright ownership and moral rights for their thesis. You may use this material in any way that is permitted by the Copyright Act or through licensing that has been assigned to the document. For uses that are not allowable under copyright legislation or licensing, you are required to seek permission.Biology--MolecularBiochemistryPhysics--Atomicquantum information processingbiological electron transferquantum biologydoctoral thesis10.11575/PRISM/27114