Date of Defense
9-4-2026 11:00 AM
Location
Microsoft Teams
Document Type
Dissertation Defense
Degree Name
Doctor of Philosophy in Chemistry
College
COS
Department
Chemistry
First Advisor
Prof. Mohamad Toutounji
Keywords
Open Quantum Systems, Non-Markovain, Non-Hermitian Dynamics, Viral Infection dynamics, Quantum Biology.
Abstract
The emerging field of quantum biology explores whether non-trivial quantum effects such as entanglement, tunnelling, and environmentally induced memory can contribute meaningfully to biological function alongside classical mechanisms. While such effects have been explored in photosynthesis, enzyme catalysis, and olfaction, their potential relevance to virology remains largely unexplored. Viruses, which straddle the boundary between living and non-living matter, provide a particularly compelling testbed for this inquiry. This thesis investigates a quantum-dynamical paradigm for viral entry, proposing that the earliest stage of SARS-CoV-2 infection may involve vibrationally assisted electron transfer (VA-ET) between the viral Spike protein and the host cell's angiotensin-converting enzyme 2 (ACE2) receptor, mediated by the cellular membrane. The Spike-ACE2 interaction is the critical first step in the infection cascade, and here it is analyzed in direct analogy with vibration-assisted mechanisms proposed for olfaction. The work employs the non-Markovian quantum state diffusion (NMQSD) formalism, a specialized form of the non-Markovian stochastic Schrödinger equation (NMSSE) to simulate electron transfer in a series of spin-boson type models that systematically incorporate harmonic, structured, anharmonic, and non-Condon environmental couplings. The central findings show that tunnelling efficiency is sharply controlled by resonance: when selected vibrational modes of the Spike protein are tuned to the energy gap between donor and acceptor sites on ACE2, VA-ET is significantly enhanced, whereas off-resonant, high-frequency modes promote decoherence and suppress transfer. Comparative simulations reveal that the physical character of the environment is crucial. A more biophysically realistic anharmonic bath, modelled using Morse oscillators and Poissonian jump noise, fundamentally reshapes electron-transfer probabilities, particularly in weak-coupling regimes, thereby exposing the limitations of standard harmonic, Gaussian approximations. On-Markovian environmental memory yields physically consistent dynamics, maintaining positive populations even in intermediate-to-strong coupling regimes, whereas Markovian treatments can sometimes produce unphysical negative populations. Furthermore, incorporating non-Condon (off-diagonal) system–bath coupling demonstrates that nuclear motion can effectively gate the tunnelling matrix element, enhancing the tunnelling rate and sharpening frequency selectivity beyond what is captured by purely dephasing (diagonal) approximations.
Included in
NON-MARKOVIAN QUANTUM STATE DIFFUSION FOR ELECTRON TRANSFER IN THE BIOLOGICAL COMPLEXES
Microsoft Teams
The emerging field of quantum biology explores whether non-trivial quantum effects such as entanglement, tunnelling, and environmentally induced memory can contribute meaningfully to biological function alongside classical mechanisms. While such effects have been explored in photosynthesis, enzyme catalysis, and olfaction, their potential relevance to virology remains largely unexplored. Viruses, which straddle the boundary between living and non-living matter, provide a particularly compelling testbed for this inquiry. This thesis investigates a quantum-dynamical paradigm for viral entry, proposing that the earliest stage of SARS-CoV-2 infection may involve vibrationally assisted electron transfer (VA-ET) between the viral Spike protein and the host cell's angiotensin-converting enzyme 2 (ACE2) receptor, mediated by the cellular membrane. The Spike-ACE2 interaction is the critical first step in the infection cascade, and here it is analyzed in direct analogy with vibration-assisted mechanisms proposed for olfaction. The work employs the non-Markovian quantum state diffusion (NMQSD) formalism, a specialized form of the non-Markovian stochastic Schrödinger equation (NMSSE) to simulate electron transfer in a series of spin-boson type models that systematically incorporate harmonic, structured, anharmonic, and non-Condon environmental couplings. The central findings show that tunnelling efficiency is sharply controlled by resonance: when selected vibrational modes of the Spike protein are tuned to the energy gap between donor and acceptor sites on ACE2, VA-ET is significantly enhanced, whereas off-resonant, high-frequency modes promote decoherence and suppress transfer. Comparative simulations reveal that the physical character of the environment is crucial. A more biophysically realistic anharmonic bath, modelled using Morse oscillators and Poissonian jump noise, fundamentally reshapes electron-transfer probabilities, particularly in weak-coupling regimes, thereby exposing the limitations of standard harmonic, Gaussian approximations. On-Markovian environmental memory yields physically consistent dynamics, maintaining positive populations even in intermediate-to-strong coupling regimes, whereas Markovian treatments can sometimes produce unphysical negative populations. Furthermore, incorporating non-Condon (off-diagonal) system–bath coupling demonstrates that nuclear motion can effectively gate the tunnelling matrix element, enhancing the tunnelling rate and sharpening frequency selectivity beyond what is captured by purely dephasing (diagonal) approximations.