The 219th R-CCS Cafe - part 3

Time-resolved XFEL methodology facilitates elucidation of molecular structures with its reaction dynamics. Short pulses of relevant timescales are employed to observe the molecular motions of biomolecular reactions. Here the change in difference density corresponding to spatial variations of atomic coordinate during femtosecond temporal pulses are captured and modelled. The relative density of atomic coordinates is built upon the reference resting state to assess the reaction dynamics which generally complements the motions as observed in molecular dynamics trajectories. In this study the objective is to identify residual correspondence between initial dark state and other light simulated states. Subsequently molecular co-ordinates corresponding to observed difference density are extracted from molecular dynamics trajectory and aligned with resting state. The associated data from trajectory is then fitted as altered state into electron density map with positional and group occupancy refinement. The fitted molecular model will reveal the transformation of regions upon light simulation and help elucidation of reaction kinetics captured using XFEL data. This presentation is about preliminary work that is being carried out.