NPI Nonperiodic nanoscale imaging

The Non-Periodic Imaging task of the Ultrafast Chemical Science FWP is focused on the goal of extending x-ray microscopy to the atomic level and femtosecond timescale. These efforts are paramount to the DOE mission of understanding and controlling matter. Non-periodic structure dominates nature and biology is nature’s version of nanotechnology. To master energy and information on the nanoscale and create new technologies with capabilities rivaling those of living things we need revolutionary new approaches to characterizing non-periodic structure. The development of x-ray free electron lasers (FELs) is such a revolutionary driving force.

Our program builds upon our past experiments developing single pulse coherent x-ray diffractive imaging (CXDI) (Chapman 2006), which utilizes the ultrafast and ultrabright x-ray pulses to help overcome current resolution limitations due to x-ray induced damage to the object. The electron density of the object is reconstructed from the scattered intensity data in the coherent diffraction pattern using lensless imaging techniques based on iterative phase retrieval techniques (Fienup 1982; Marchesini 2007).

Despite the rapid progress made in CXDI, many basic questions remain regarding the optimum acquisition of single-shot diffraction data, in particular for the assembly of 3D structures, from aerosols, biomolecules, viruses, or clusters. At the core of non-periodic structural studies with x-ray lasers are the algorithms necessary for simulations of experimental design and for the recovery of structural information. Improvements in the methods for delivery of sample material to x-ray lasers can be made. Nanoflow liquid microjets with sub-micron diameters are necessary to accommodate sample delivery into the submicron x-ray focus now achievable. To best take advantage of the time structure of LCLS pulses to probe dynamic biomolecular structure, improved photoactivation and chemical mixing schemes are necessary for time-resolved diffraction experiments of crystallography and fluctuation scattering.

The Non-Periodic Imaging team is devoted to tackling these and other unforeseen challenges by developing the basic theoretical and experimental science necessary to open entirely new fields of non-periodic structural study with x-ray lasers.

Aerosol Morphology

In our quest toward quantitative single molecule and nanoparticle imaging, we explore the (1) most basic structures (single spheres) and (2) complex unknown structures comprised of known component size and chemical composition – i.e., aerosol self-assembled clusters of monodisperse spheres or rods. This system allows us to address the most fundamental questions in single particle diffractive imaging, develop and test imaging algorithms, and lay the groundwork to interpreting the complex structures such as (3) viruses and cells or (4) airborne particulate matter, like soot.

Single Particle Coherent Diffractive Imaging with a Soft X-ray Free Electron Laser: Towards Soot Aerosol Morphology

Bogan, M., Starodub, D., Hampton, C. Y., Sierra R. G.
J. Phys. B: AMO 43 194013, (2010) -invited article to the SPECIAL ISSUE: INTENSE X-RAY SCIENCE: THE FIRST 5 YEARS OF FLASH » link to article


We comprehensively reviewed the aerosol methods used for single particle imaging at FLASH that laid the groundwork for the first LCLS experiments. We predicted the capability of FELs to extract structural information from airborne soot, completely unique particles that cannot be imaged at high resolution any other way. We simulated CXDI of combustion particle (soot) morphology and introduced the concept of extracting radius of gyration of fractal aggregates from single pulse x-ray diffraction data.

Fractal morphology, imaging and mass spectrometry of single aerosol particles in flight

ND Loh, CY Hampton, AV Martin, D Starodub, RG Sierra, A Barty, A Aquila, J Schulz, L Lomb, J Steinbrener, RL Shoeman, S Kassemeyer, C Bostedt, J Bozek, SW Epp, B Erk, R Hartmann, D Rolles, A Rudenko, B Rudek, L Foucar, N Kimmel, G Weidenspointner, G Hauser, P Holl, E Pedersoli, M Liang, MM Hunter, L Gumprecht, N Coppola, C Wunderer, H Graafsma, FRNC Maia, T Ekeberg, M Hantke, H Fleckenstein, H Hirsemann, K Nass, TA White, HJ Tobias, GR Farquar, WH Benner, SP Hau-Riege, C Reich, A Hartmann, H Soltau, S Marchesini, S Bajt, M Barthelmess, P Bucksbaum, KO Hodgson, L Strüder, J Ullrich, M Frank, I Schlichting, HN Chapman and MJ Bogan Nature, 486, 513-517 (2012) » link to article

SLAC Press Release: X-ray Vision Exposes Aerosol Structures

DOE PULSE Highlight: First detailed images of airborne soot show surprising complexity

SLAC Press Release: X-ray Vision Exposes Aerosol Structures
DOE PULSE Highlight: First detailed images of airborne soot show surprising complexity


The morphology of micrometer-size particulate matter is of critical importance in fields ranging from toxicology to climate science, yet these properties are surprisingly difficult to measure in the particles’ native environment. Electron microscopy requires collection of particles on a substrate; visible light scattering provides insufficient resolution; and X-ray synchrotron studies have been limited to ensembles of particles. Here we demonstrate an in situ method for imaging individual sub-micrometre particles to nanometre resolution in their native environment, using intense, coherent X-ray pulses from the Linac Coherent Light Source free-electron laser. We introduced individual aerosol particles into the pulsed X-ray beam, which is sufficiently intense that diffraction from individual particles can be measured for morphological analysis. At the same time, ion fragments ejected from the beam were analysed using mass spectrometry, to determine the composition of single aerosol particles. Our results show the extent of internal dilation symmetry of individual soot particles subject to non-equilibrium aggregation, and the surprisingly large variability in their fractal dimensions. More broadly, our methods can be extended to resolve both static and dynamic morphology of general ensembles of disordered particles. Such general morphology has implications in topics such as solvent accessibilities in proteins, vibrational energy transfer by the hydrodynamic interaction of amino acids, and large-scale production of nanoscale structures by flame synthesis. A primary long-term goal of the research is to take snapshots of airborne particles as they change their size, shape and chemical make-up in response to their environment.

Single-shot fractal dimension determination

From Loh D; et al Nature 2012 486 513-517 (2012) » link to article

First demonstration that the slope of radially averaged single-shot diffraction patterns can be used to extract the fractal dimension of single airborne particles in flight.


Serial Femtosecond Crystallography (SFX)

The advent of short pulse X-ray free electron lasers (XFELs) offers a completely new crystallography paradigm by enabling SFX. Diffraction patterns from millions of individual protein microcrystals can be captured one-at-a-time before X-ray damage manifests itself (see Chapman et al., 2011).

Apparatus and Method for Nanoflow Serial Femtosecond X-ray Protein Crystallography

Bogan, M.; Sierra, R.G.; Laksmono, H.L. Provisional Patent, (2012)

Nanoflow Electrospinning Serial Femtosecond Crystallography

Sierra, RG, Laksmono, H, Kern, J, Hattne, J, Alonso-Mori, R, Gloeckner, C, Tran, R, Hellmich, J, Lassalle-Kaiser, B, Schafer, DW, Sellberg, J, McQueen, TA, Fry, A, Messerschmidt, M, Miahnahri, A, Seibert, MM, Hampton, CY, Starodub, D, Loh, NTD, Zwart, PH, Milathianaki, D, White, WE, Adam, PD, Boutet, S, Williams, GJ, Messinger, J, Sauter, NK, Zouni, A, Bergmann, U, Yano, J, Yachandra, VK, & Bogan, MJ. Acta Crystallographica D, accepted (2012)

We report a sample delivery method that reduces sample consumption by 60-100 times from the current method while meeting the unique needs of SFX for structural biology.

High-resolution protein structure determination by serial femtosecond crystallography

S. Boutet et al Science 337,362-364 (2012) » link to article

SFX, using the Coherent X-ray Imaging (CXI) endstation (Boutet & Williams, 2010) at the Linac Coherent Light Source (LCLS), produced high resolution (<2Å) protein structures.

Room temperature femtosecond X-ray diffraction of photosystem II microcrystals

J. Kern et al PNAS, 109, 9721-9726 (2012) » link to article

The first reported demonstration of SFX on the complex membrane protein Photosystem II. Data was collected using our patented nanoflow liquid jet apparatus.

Femtosecond x‐ray protein nanocrystallography


H. Chapman et al Nature, 470, 73-77 (2011) » link to article

The first demonstration of serial femtosecond crystallography with an X-ray laser.

Night Vision Goggle Crystallography

“Seen Around SLAC” features one of our Arizona state University collaborators growing Photosystem crystals in a darkroom setup in our B40 lab

Algorithm Development for Single Particle Diffraction

At the core of non-periodic structural studies with x-ray lasers are the algorithms necessary for simulations of experimental design and for the recovery of structural information. As of 2012, no 3D structure has been published from single shot diffraction patterns of non-crystalline material collected at LCLS. Our cryptotomography demonstration is still the only 3D structure reported from FEL single shots of identical particles in random orientations. For single-shot data analysis a limitation lies in the size of object amenable to iterative phase retrieval. Overcoming the missing data problem present in CXDI would enable single-shot imaging of objects larger than 500 nm, such as cells or airborne particulate matter. Taking advantage of correlated x-ray scattering for single particle structure remains intensively studied theoretically and we are implementing it in practice with LCLS data.

Cryptotomography: Reconstructing 3D fourier intensities from randomly oriented single-shot diffraction patterns


Loh, D; Bogan, MJ et al, Physical Review Letters 104, 225501 (2010) » link to article

First demonstration of 3D reconstruction from single-shot FEL data.

Reconstruction of the electron density of molecules with single axis alignment

Starodub D; et al, Proceedings SPIE: Image Reconstruction from Incomplete Data 7800O (2010) » link to article

Diffraction from the individual molecules of a molecular beam, aligned parallel to a single axis by a strong electric field or other means, has been proposed as a means of structure determination of individual molecules. Starodub_GroEL_SPIE As in fiber diffraction, all the information extractable is contained in a diffraction pattern from incidence of the diffracting beam normal to the molecular alignment axis. We present two methods of structure solution for this case. One is based on the iterative projection algorithms for phase retrieval applied to the coefficients of the cylindrical harmonic expansion of the molecular electron density. Another is the holographic approach utilizing presence of the strongly scattering reference atom for a specific molecule.