7,460 research outputs found
Expansion-maximization-compression algorithm with spherical harmonics for single particle imaging with X-ray lasers
In 3D single particle imaging with X-ray free-electron lasers, particle
orientation is not recorded during measurement but is instead recovered as a
necessary step in the reconstruction of a 3D image from the diffraction data.
Here we use harmonic analysis on the sphere to cleanly separate the angu- lar
and radial degrees of freedom of this problem, providing new opportunities to
efficiently use data and computational resources. We develop the
Expansion-Maximization-Compression algorithm into a shell-by-shell approach and
implement an angular bandwidth limit that can be gradually raised during the
reconstruction. We study the minimum number of patterns and minimum rotation
sampling required for a desired angular and radial resolution. These extensions
provide new av- enues to improve computational efficiency and speed of
convergence, which are critically important considering the very large datasets
expected from experiment
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
The pypadf package: computing the pair-angle distribution function from fluctuation scattering data
The pair-angle distribution function (PADF) is a three- and four-atom
correlation function that can characterise the local angular structure of
disordered materials, particles or nanocrystalline materials. The PADF can be
measured by x-ray or electron fluctuation diffraction experiments, which can be
collected by scanning a small beam across a structurally disordered sample or
flowing a sample across the beam path. It is a natural generalisation of the
established pair-distribution methods, which do not provide angular
information. This software package provides tools to calculate the PADF from
from fluctuation diffraction data. The package includes tools for calculating
the intensity correlation function, which is a necessary step in the PADF
calculation and also the basis for other fluctuation scattering techniques.Comment: 21 pages, 3 figure
Anatomical Parcellation of Cortical Language Sites
Anatomical labeling of cerebral cortical stimulation (CSM) sites is necessary for intelligent computer querying of a rich and unique experimental database examining neural substrates underlying human language production. To this end, we have developed a parcellation scheme for the lateral surface of the human cerebral cortex. We then compared results generated utilizing this approach to those generated using an alternative method implemented in the Talairach Daemon
Realizing Exactly Solvable SU(N) Magnets with Thermal Atoms
We show that thermal fermionic alkaline-earth atoms in a flat-bottom trap
allow one to robustly implement a spin model displaying two symmetries: the
symmetry that permutes atoms occupying different vibrational levels of
the trap and the SU() symmetry associated with nuclear spin states. The
high symmetry makes the model exactly solvable, which, in turn, enables the
analytic study of dynamical processes such as spin diffusion in this SU()
system. We also show how to use this system to generate entangled states that
allow for Heisenberg-limited metrology. This highly symmetric spin model should
be experimentally realizable even when the vibrational levels are occupied
according to a high-temperature thermal or an arbitrary non-thermal
distribution.Comment: 12 pages, 5 figures (including supplemental materials
Dissociation of Action and Object Naming: Evidence From Cortical Stimulation Mapping
This cortical stimulation mapping study investigates the neural representation of action and object naming. Data from 13 neurosurgical subjects undergoing awake cortical mapping is presented. Our findings indicate clear evidence of differential disruption of noun and verb naming in the context of this naming task. At the individual level, evidence was found for punctuate regions of perisylvian cortex subserving noun and verb function. Across subjects, however, the location of these sites varied. This finding may help explain discrepancies between lesion and functional imaging studies of noun and verb naming. In addition, an alternative coding of these data served to highlight the grammatical class vulnerability of the target response. The use of this coding scheme implicates a role for the supramarginal gyrus in verb-naming behavior. These data are discussed with respect to a functional-anatomical pathway underlying verb naming
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
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