The featured item this time is “Structure from Fleeting Illumination of Faint Spinning Objects in Flight with Application to Single Molecules” by Russell Fung and co-authors at U Wisconsin Milwaukee.
The promise of solving atomic-resolution 3D structure of biological proteins with X-ray Free Electron Lasers has several obstacles. First one is to have fast enough x-ray pulse to image molecules before it starts to undergo “Coulomb explosion”. But even that is not sufficient to produce atomic-scale structure due to low scattering cross-section of hard x-rays – so the experiment will need to be repeated many (thousands?) times to improve statistics. Luckily, protein molecules are identical, so the fundamental 3D structure of the sample could be considered the same – however, the orientation of protein molecule is going to be different each time.
There are two ways to solve the “random orientation” problem – one is to try to align the molecule, for example with a laser beam. However this has to be done with a very high precision and is difficult to achieve in practice. Another approach is to do experiment thousands of times with random orientations of molecules, catalogue all resulting projections, and then use mathematical algorithms to “fold” the projections into a unique 3D object that is consistent with all resulting projections.
Russel Fung et al. provide an algorithm that does just that – by simulating realistic conditions of 4th generation synchrotron source, X-ray Free Electron Laser, with collection of 100,000 photons, 72,000 repeated diffraction patterns from single shot experiments and scattering rates as low as 0.01 photons per pixel at large wavevectors corresponding to 1.8 Angstrom.
The result of folding using Generative Topographic Mapping for protein chignolin in random orientations is shown in figure above, for 3D movie of this reconstructed molecule see Abbas Ourmazd’s webpage at UW Milwaukee.
A shortlived 
Lindenberg and coworkers were able to look at both high-angle and small-angle diffuse scattering resulting in ablation process in this time-resolved mode. Their data indicates presence of short-lived nanoscale voids (shown in green in the figure on the right) in the liquid state caused by the laser pulse, and these voids merge together to form larger voids over the timescale of 20 ps or so – claims supported by molecular dynamics simulations. While their data was taken in reciprocal space, by recording ensemble-averaged structure factor S(q) at various time delays from the laser pulse, in the future one could envision fully inverting the speckle patterns shown in the figure above, to obtain a real-space images of the nanoscale voids.
