Ultrafast structural dynamics by crystallography and coherent control

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The van Thor group specialises in the investigating ultrafast structural dynamics of light-sensitive proteins,elucidating the nuclear and electronic dynamics in key biological reactions. The advent of fourth-generationlight sources, X-ray free electron lasers (XFELS), has allowed unprecedented temporal resolution ofangstrom wavelength for pump-probe spectroscopy. The group is at the forefront of utilising theseinstruments in developing novel experimental ultrafast techniques, specifically time-resolved serialfemtosecond crystallography (TR-SFX) and the corresponding theory.1,2 The objective of this PhD projectis to build upon this work and conduct experiments supported by theory to elucidate structural dynamics bycoherent control.It is known that large vibrational coherence is generated in both the ground and excited states, followingoptical excitation of biological proteins.1 Suppressing or enhancing coherence, can lead to manipulation ofthe populations in states and reaction pathways. Optical control is a method whereby changing thecharacteristics of the laser pulses can manipulate the coherent amplitude in both ground and excited states.The peak power, pulse duration, carrier frequency and second-order dispersion of a pump pulse have allbeen shown to impact coherent amplitude.2,3 Additionally, it has been recently observed that secondary(dump) pulses can enhance coherence in the ground state.The initial work of this project will be to develop theoretical simulations in collaboration with the Buckupgroup Heidelberg, to compliment historic XFEL crystallographic experimentation. The simulations will thenbe used to provide theoretical support for future experimental results and influence experimental design.The simulations employ a non-perturbative time-dependant density matrix model and monitors the transienteffect after perturbation from an external electric field (laser pulse).4 The simulations will allow full controlof the characterisation of multiple laser pulses, such that all facets of optical control described above canbe investigated. Analysis of the coherence can be discerned by a transformation of the density matrix tothe semi-classical Wigner phase space representation and coherent amplitudes resolved.5Upon completion of the simulations, work will begin on developing the apparatus to allow pulse shaping tomanipulate the pulse characteristics in the home laser laboratory. Employing ultrafast transient absorptionspectroscopy technique, combined with active pulse shaping will allow coherent control of moleculardynamics by impulsive Raman spectroscopy. Furthermore, the optimisation of pulse characteristics forcoherent control can then be implemented in TR-SFX experiments with beam times at XFELs.In addition to optical control, coherence can be controlled via the structural, symmetry and directionalproperties of protein crystals. Two dimensional electronic and infrared spectroscopy has been identified astechniques which could discern the effects these properties have on vibrational coherence.6This project hopes to elucidate structural dynamics by coherent control, incorporating multiple experimentaltechniques with theory. Investigating multiple facets of coherent control both optically and structurally.