Monday, October 26, 2009

Simulating quantum dynamics in biomolecular excited states

At the Quantum Efficiency workshop in the BlackForest Gerhard Stock (who has just moved from Frankfurt back to Freiburg) gave an excellent talk, Quantum signatures in biomolecular processes. Here are some of my notes.

Strategies to describe complex systems.

Biomolecular dynamics: water through the membrane protein can be modelled well with state-of-the art molecular dynamics simulations.

In such simulations how does one deal with the fact that many bonds are stiff enough that they are only in the vibrational ground state at room temperature? Approximate stiff bonds as fixed.

Rhodopsin: the primary event in vision
Vibrationally coherent photochemistry (lastest experiments by Prokhorenko and Miller, Science 2006) investigated the photo-isomerisation reaction retinal.

Minimal model [Hahn and Stock, JPC B 2000].
A two state model with two vibrational models
Co-ordinate dependent non-adiabatic couplings lead to conical intersection. One can solve the quantum dynamics exactly. Successful simulation of pump-probe experiments up to psec.

Origin of coherent oscillations? Beating between vibronic levels.

Time-dependent wave packet dynamics.
Completely delocalised dynamics on the ground state S0 PES.
Is this quantum or classical? Could be either.

Chaotic vs. regular dynamics.

What features determine the reaction speed and quantum yield?
Interact system with a bath using Redfield theory.
Two alternative couplings to bath.
Conical intersection is crucial.
Mechanism of photochemical funnel CPL 2003.
Environment is important for irreversible transport through the conical intersection.
Subtle interplay of coherence and dissipative localisation.

Vibrational Energy flow in biomolecules
Motivated by Hamm's experiments.
PRL 2009.
Trialanine is the model molecule.

Resonant energy transfer (RET) can describe energy transfer between
neigbouring amide groups. Semi-classical works well for RET because energy levels are close
but not for energy relaxation.

For bilinear coupling, quantum and classical are only different in the populations of levels associated with states.

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