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.

More coherent x-ray lens-less image reconstructions

New paper in Science by Pierre Thibault et al. “High-Resolution Scanning X-ray Diffraction Microscopy” Science 321, 379 (2008).

Authors use an approach identical to ptychography  to demonstrate the power of the technique by reconstructing the Fresnel Zone Plate – similar to work by Rodenburg et al., PRL 98, 034801 (2007).

John Miao and his UCLA group has used lensless imaging to reconstruct image of a single virus:

C. Song et al., “Quantitative Imaging of Single, Unstained Viruses with Coherent X-rays” arXiv:0806.2875.

And Stadler et al. “Hard X Ray Holographic Diffraction Imaging” Phys. Rev. Lett. 100, 245503 (2008) show that the x-ray holographic approach similar to the one previously used by Eisebitt et al., Nature 432, 885 (2004) works in hard-xray regime as should be expected. They cleverly used five carefully positioned nanoparticles as the negative sources of reference beam, and successfully demonstrated that letter “P” can be reconstructed, adding to an impressive alphabet of reconstructed letters and logos. While use of hard x-rays paves the road for imaging of thick speciments, it’s not clear if one could take advantage of the same principle in high-angle diffraction geometry, which is where real action is for hard x-rays.

Nanoparticle Self-assembly with DNA

Image on the left is the cover of Jan. 31 issue of Nature.

Anyone who took high school chemistry has played with “sticks and balls” models of molecules or crystalline atoms. There are magnetic toy sets which allow kids to assemble their own version of crystals.

A similar feat, but on nanoscale, was accomplished by two groups – one at Brookhaven (Nykypanchuk et. al  Nature 451, 549-552 (2008)) and another at Northwestern (Park et. al, Nature 451, 553-556 (2008)).

The basic idea behind these two experiments is to graft different strands of DNA molecules onto particles, creating two “species” of particles with complimentary pairs of DNA strands. These two different types of strands can merge together into a double helix at high temperatures, making a strong connection between particles of the opposite species. The result is a cubic structure, similar to ion salts.

The nanoparticle crystals held together by DNA molecules are rather fragile, and most of volume is occupied by water. The typical size of the unit cell is on the order of 35-50 nm, with particle size just 10 nm in size. The nanoparticles therefore occupy only a tiny fraction of the total crystal volume, with density of such “fluffy” crystals less than milk foam in your latte.

DNA capture and recapture with nanopores

The featured article is “Recapturing and trapping single molecules with a solid-state nanopore” by Gershow, M. & Golovchenko, J. A. Nature Nanotech. 2, 775–779 (2007).

The idea behind nanopore-based DNA sequencing is relatively simple – pass a DNA molecule through a nanopore channel, sort of the same way you pass a thread through an eye of the needle. As the DNA is passing through the pore, it can be “read out” by looking for specific signatures of the four bases in, for example, electrical capacitance. Experimental implementation of this idea is of course very challenging.

Gershow and Golovchenko demonstrate that they have ability to “suck” the DNA molecule back into the pore, sufficiently long time after it left the pore. The figure above demonstrates this process schematically.

See also a News and Views by Derek Stein, as well as “Colloquium” review of DNA sequencing approaches in Review of Modern Physics paper by DiVentra and Zwolak.