3D object reconstruction from random orientations

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.

sub-picosecond movies of nucleation dynamics

A shortlived SPPS facility is still producing papers – this week it’s the PRL paper by Aaron Lindenberg and some 28 co-authors ” X-Ray Diffuse Scattering Measurements of Nucleation Dynamics at Femtosecond Resolution” Phys. Rev. Lett. 100, 135502 (2008).

This is yet another pump-probe experiment, where pump is a femtosecond laser which ablates/melts a crystal, and a probe is a sub-picosecond x-ray pulse from SPPS. X-ray probe pulse length is still a limiting parameter in overall time resolution of such pump-probe setups. This experiment had a time resolution of 700 fs, but in the near future at XFEL facilities such as LCLS the time resolution will approach tens of femtosecond.

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.

XFEL trifecta in Science, Nature

Last week was the “perfect storm” of XFEL ultrafast science, with four papers in Nature and Science:

Nature featured a paper by Henry Chapman et al. on Femtosecond time-delay X-ray Holography. By recording an interference pattern of a particle and it’s mirror image it is possible to record an ultrafast “explosive” motion of the particle due to exposure of the x-ray beam. It’s the ultimate pump-probe experiment where both pump and probe are one and the same.
This paper is accompanied by News and Views article “Femtophysics: Double vision” by Andrea Cavalleri.

Science has two review papers out – one is “Harnessing Attosecond Science in the Quest for Coherent X-rays” by Kaptey et. al from Margaret Murnane’s group at Colorado Boulder.

There is also a Review paper by Phil Bucksbaum on “The Future of Attosecond Spectroscopy”.

Thee two papers are part of the special section on attosecond spectroscopy, also featured as a cover story.

Ultrafast work at SPPS

This week’s item is inspired by my recent visit to Stanford, in anticipation of the world’s first x-ray free electron laser – LCLS, which will open in 2009. LCLS is a facility that will feature ultrashort (200 fs) x-ray pulses that are fully coherent in transverse directions, and will be using one third of a 3-km linear accelerator as the source of electrons that will be used for “lasing” in a total of about 100m of undulator. In comparison, current third generation hard x-ray sources like APS, ESRF or SPRING-8 use undulators that are only a couple of meters long, and pulses that are about 1,000 times longer – on the order of 100 ps.

In preparation to LCLS, scientists built a temporary facility called Sub-Picosecond Pulse Source (SPPS). It used SLAC’s LINAC electron beam outfitted with a relatively short undulator. The total flux was nowhere near projected LCLS values or even sources like APS – in fact (as reported here previously) when LCLS becomes operational it will produce more x-rays in the first 10 seconds than SPPS produced in its entire 3-year lifetime. But SPPS was a unique source of sub-ps x-rays, and produced some really interesting science. One such result was featured in Science earlier this year: a report by D. Fritz et al., includes almost 40 collaborators from 20 different institutions.

The basic idea of experiment is pump-probe – hitting Bi crystal with a ultrafast powerful laser and use x-rays to probe the lattice structure some short time later. Because both laser and x-ray pulses are sub-ps, one can in principle shoot a movie of structural lattice dynamics in response to the initial laser pulse, with sub-ps time resolution – something other x-ray sources currently cannot do. But in order to do this, one has to be able to vary the delay between laser and x-ray pulse – which was problematic at SPPS due to jitter, which results in random delay between the two pulses. However, using a clever time-tagging technique, the jitter was used to the experiment’s advantage – by figuring out the time delay between the two pulses that resulted from jitter for each pulse, scientists were able to use jitter to scan the time delay – even though the time of arrival is highly random, this randomness provides a way for varying the delay.

Coherent X-ray imaging and dynamics

This week’s journal club item is a Science magazine review article by Gaffney and Chapman on imaging of atomic structure and dynamics using coherent x-ray beams, ultrafast x-ray beams and the combination of the two. Even though most of the coherent x-ray imaging part of the review is understandably focused on single-molecule imaging, the paper provides a very nice overview of the extremely bright future, and also of some key challenges.

This quote is quite remarkable, in providing a nice comparison of future vs. present/past sources: “At the LCLS, the integrated x-ray production in 10 s of lasing will exceed the total x-ray photon production at the SPPS during its 3-year lifetime.”

It’s also interesting to note that the review is published in Science, a relative newcomer to coherent x-ray field heavily dominated by Nature and more recently also by Nature Physics.