71 research outputs found
Single molecule imaging with longer x-ray laser pulses
During the last five years, serial femtosecond crystallography using x-ray
laser pulses has developed into a powerful technique for determining the atomic
structures of protein molecules from micrometer and sub-micrometer sized
crystals. One of the key reasons for this success is the "self-gating" pulse
effect, whereby the x-ray laser pulses do not need to outrun all radiation
damage processes. Instead, x-ray induced damage terminates the Bragg
diffraction prior to the pulse completing its passage through the sample, as if
the Bragg diffraction was generated by a shorter pulse of equal intensity. As a
result, serial femtosecond crystallography does not need to be performed with
pulses as short as 5--10 fs, as once thought, but can succeed for pulses
50--100 fs in duration. We show here that a similar gating effect applies to
single molecule diffraction with respect to spatially uncorrelated damage
processes like ionization and ion diffusion. The effect is clearly seen in
calculations of the diffraction contrast, by calculating the diffraction of
average structure separately to the diffraction from statistical fluctuations
of the structure due to damage ("damage noise"). Our results suggest that
sub-nanometer single molecule imaging with 30--50 fs pulses, like those
produced at currently operating facilities, should not yet be ruled out. The
theory we present opens up new experimental avenues to measure the impact of
damage on single particle diffraction, which is needed to test damage models
and to identify optimal imaging conditions.Comment: 23 pages; 5 figure
MolDStruct: modelling the dynamics and structure of matter exposed to ultrafast X-ray lasers with hybrid collisional-radiative/molecular dynamics
We describe a method to compute photon-matter interaction and atomic dynamics
with X-ray lasers using a hybrid code based on classical molecular dynamics and
collisional-radiative calculations. The forces between the atoms are
dynamically computed based on changes to their electronic occupations and the
free electron cloud created due to the irradiation of photons in the X-ray
spectrum. The rapid transition from neutral solid matter to dense plasma phase
allows the use of screened potentials, which reduces the number of non-bonded
interactions required to compute. In combination with parallelisation through
domain decomposition, large-scale molecular dynamics and ionisation induced by
X-ray lasers can be followed. This method is applicable for large enough
samples (solids, liquids, proteins, viruses, atomic clusters and crystals) that
when exposed to an X-ray laser pulse turn into a plasma in the first few
femtoseconds of the interaction. We show several examples of the applicability
of the method and we quantify the sizes that the method is suitable for. For
large systems, we investigate non-thermal heating and scattering of bulk water,
which we compare to previous experiments. We simulate molecular dynamics of a
protein crystal induced by an X-ray pump, X-ray probe scheme, and find good
agreement of the damage dynamics with experiments. For single particle imaging,
we simulate ultrafast dynamics of a methane cluster exposed to a femtosecond
X-ray laser. In the context of coherent diffractive imaging we study the
fragmentation as given by an X-ray pump X-ray probe setup to understand the
evolution of radiation damage.Comment: 12 pages, 11 figures, 50 reference
Rapidity gaps at HERA and the Tevatron from soft colour exchanges
Models based on soft colour exchanges to rearrange colour strings in the
final state provide a general framework for both diffractive and
non-diffractive events in ep and hadron-hadron collisions. We study two such
models and find that they can reproduce rapidity gap data from both HERA and
the Tevatron. We also discuss the influence of parton cascades and multiple
interactions on the results.Comment: 4 pages, 4 EPS figures, presented at UK Phenomenology Workshop on
Collider Physics, Durham. Uses iopart.cl
Progress and Poverty—1965 Version
The first hard X-ray laser, the Linac Coherent Light Source (LCLS), produces 120 shots per second. Particles injected into the X-ray beam are hit randomly and in unknown orientations by the extremely intense X-ray pulses, where the femtosecond-duration X-ray pulses diffract from the sample before the particle structure is significantly changed even though the sample is ultimately destroyed by the deposited X-ray energy. Single particle X-ray diffraction experiments generate data at the FEL repetition rate, resulting in more than 400,000 detector readouts in an hour, the data stream during an experiment contains blank frames mixed with hits on single particles, clusters and contaminants. The diffraction signal is generally weak and it is superimposed on a low but continually fluctuating background signal, originating from photon noise in the beam line and electronic noise from the detector. Meanwhile, explosion of the sample creates fragments with a characteristic signature. Here, we describe methods based on rapid image analysis combined with ion Time-of-Flight (ToF) spectroscopy of the fragments to achieve an efficient, automated and unsupervised sorting of diffraction data. The studies described here form a basis for the development of real-time frame rejection methods, e. g. for the European XFEL, which is expected to produce 100 million pulses per hour. (C)2014 Optical Society of Americ
A statistical approach to detect protein complexes at X-ray free electron laser facilities
The Flash X-ray Imaging (FXI) technique, under development at X-ray free electron lasers (XFEL), aims to achieve structure determination based on diffraction from individual macromolecular complexes. We report an FXI study on the first protein complex-RNA polymerase II-ever injected at an XFEL. A successful 3D reconstruction requires a high number of observations of the sample in various orientations. The measured diffraction signal for many shots can be comparable to background. Here we present a robust and highly sensitive hit-identification method based on automated modeling of beamline background through photon statistics. It can operate at controlled false positive hit-rate of 3 x10(-5). We demonstrate its power in determining particle hits and validate our findings against an independent hit-identification approach based on ion time-of-flight spectra. We also validate the advantages of our method over simpler hit-identification schemes via tests on other samples and using computer simulations, showing a doubled hit-identification power
Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source
Single particle diffractive imaging data from Rice Dwarf Virus (RDV) were recorded using the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS). RDV was chosen as it is a wellcharacterized model system, useful for proof-of-principle experiments, system optimization and algorithm development. RDV, an icosahedral virus of about 70 nm in diameter, was aerosolized and injected into the approximately 0.1 mu m diameter focused hard X-ray beam at the CXI instrument of LCLS. Diffraction patterns from RDV with signal to 5.9 angstrom ngstrom were recorded. The diffraction data are available through the Coherent X-ray Imaging Data Bank (CXIDB) as a resource for algorithm development, the contents of which are described here.11Ysciescopu
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Single Particle Difraction at FLASH
Single-pulse coherent diffraction patterns have been collected from randomly injected single particles with a soft X-ray free-electron laser (FEL). The intense focused FEL pulse gives a high-resolution low-noise coherent diffraction pattern of the object before that object turns into a plasma and explodes. A diffraction pattern of a single particle will only be recorded when the particle arrival into the FEL interaction region coincides with FEL pulse arrival and detector integration. The properties of the experimental apparatus coinciding with these three events set the data acquisition rate. For our single particle FLASH diffraction imaging experiments: (1) an aerodynamic lens stack prepared a particle beam that consisted of particles moving at 150-200 m/s positioned randomly in space and time, (2) the 10 fs long FEL pulses were delivered at a fixed rate, and (3) the detector was set to integrate and readout once every two seconds. The effect of these experimental parameters on the rate of data acquisition using randomly injected particles will be discussed. Overall, the ultrashort FEL pulses do not set the limit of the data acquisition, more important is the effective interaction time of the particle crossing the FEL focus, the pulse sequence structure and the detector readout rate. Example diffraction patterns of randomly injected ellipsoidal iron oxide nanoparticles in different orientations are presented. This is the first single particle diffraction data set of identical particles in different orientations collected on a shot-to-shot basis. This data set will be used to test algorithms for recovering 3D structure from single particle diffraction
Intergenerational impacts of maternal mortality: Qualitative findings from rural Malawi
Background: Maternal mortality, although largely preventable, remains unacceptably high in developing countries such as Malawi and creates a number of intergenerational impacts. Few studies have investigated the far-reaching impacts of maternal death beyond infant survival. This study demonstrates the short- and long-term impacts of maternal death on children, families, and the community in order to raise awareness of the true costs of maternal mortality and poor maternal health care in Neno, a rural and remote district in Malawi. Methods: Qualitative in-depth interviews were conducted to assess the impact of maternal mortality on child, family, and community well-being. We conducted 20 key informant interviews, 20 stakeholder interviews, and six sex-stratified focus group discussions in the seven health centers that cover the district. Transcripts were translated, coded, and analyzed in NVivo 10. Results: Participants noted a number of far-reaching impacts on orphaned children, their new caretakers, and extended families following a maternal death. Female relatives typically took on caregiving responsibilities for orphaned children, regardless of the accompanying financial hardship and frequent lack of familial or governmental support. Maternal death exacerbated children’s vulnerabilities to long-term health and social impacts related to nutrition, education, employment, early partnership, pregnancy, and caretaking. Impacts were particularly salient for female children who were often forced to take on the majority of the household responsibilities. Participants cited a number of barriers to accessing quality child health care or support services, and many were unaware of programming available to assist them in raising orphaned children or how to access these services. Conclusions: In order to both reduce preventable maternal mortality and diminish the impacts on children, extended families, and communities, our findings highlight the importance of financing and implementing universal access to emergency obstetric and neonatal care, and contraception, as well as social protection programs, including among remote populations
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