Quantum Dynamics in Biological Systems
Contributors: Aspuru-Guzik, Alan; Heller, Eric; Shakhnovich, Eugene
Published: 2012
Language: eng
Description: In the first part of this dissertation, recent efforts to understand quantum mechanical effects in biological systems are discussed. Especially, long-lived quantum coherences observed during the electronic energy transfer process in the Fenna-Matthews-Olson complex at physiological condition are studied extensively using theories of open quantum systems. In addition to the usual master equation based approaches, the effect of the protein structure is investigated in atomistic detail through the combined application of quantum chemistry and molecular dynamics simulations. To evaluate the thermalized reduced density matrix, a path-integral Monte Carlo method with a novel importance sampling approach is developed for excitons coupled to an arbitrary phonon bath at a finite temperature. In the second part of the thesis, simulations of molecular systems and applications to vibrational spectra are discussed. First, the quantum dynamics of a molecule is simulated by combining semiclassical initial value representation and density funcitonal theory with analytic derivatives. A computationally-tractable approximation to the sum-of-states formalism of Raman spectra is subsequently discussed.
Notes: Keywords: Fenna-Matthews-Olson complex, long-lived quantum coherences, molecular dynamics, path integral Monte Carlo, resonance Raman, semiclassical initial value representation.

Thesis Ph.D. Harvard University 2012