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  • 1.
    Forsberg, Björn
    Stockholm University, Faculty of Science, Department of Physics.
    Classical over-the-barrier model for ionization of poly-cyclic aromatic hydrocarbons in keV-collisions with atomic ions2011Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    We are developing a novel classical over-the barrier model for electron transfer from an in nitely thin conducting disc to a point charge projectile to model multiple electron capture in e.g. keV collisions of atomic ions with poly-cyclic aromatic hydrocarbons (PAHs). In its nal form, the present model will incorporate the polarization of the PAH molecules due to the active electron and the point charge projectile at a general angle of incidence. This will drastically improve the description of the potential barrier in comparisons with simpler versions of the model where the nite size and polarizability of the target molecule is neglected or treated in an averaged fashion. In this work we arrive at expressions for the electrostatic potential energy barrier experienced by the active electron in the two spatial orientations where the point charge projectile is located along the normal symmetry axis and in the tangent plane of the disc. Applied to coronene (C24H12) such barriers compare better with high level density functional theory (DFT) calculations than with the results from the simpler versions of the classical over-the-barrier models for atomic and spherical cluster targets. These results thus strongly supports the conducting disc approximation of PAHs. Finally we discuss the nal steps in the model development and possible extensions of the model to include less symmetric elliptical discs or spherical caps.

  • 2.
    Forsberg, Björn O.
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Aibara, Shintaro
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Kimanius, Dari
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Paul, Bijoya
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Lindahl, Erik
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Amunts, Alexey
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Cryo-EM reconstruction of the chlororibosome to 3.2 angstrom resolution within 24 h2017In: IUCrJ, ISSN 0972-6918, E-ISSN 2052-2525, Vol. 4, 723-727 p.Article in journal (Refereed)
    Abstract [en]

    The introduction of direct detectors and the automation of data collection in cryo-EM have led to a surge in data, creating new opportunities for advancing computational processing. In particular, on-the-fly workflows that connect data collection with three-dimensional reconstruction would be valuable for more efficient use of cryo-EM and its application as a sample-screening tool. Here, accelerated on-the-fly analysis is reported with optimized organization of the data-processing tools, image acquisition and particle alignment that make it possible to reconstruct the three-dimensional density of the 70S chlororibosome to 3.2 angstrom resolution within 24 h of tissue harvesting. It is also shown that it is possible to achieve even faster processing at comparable quality by imposing some limits to data use, as illustrated by a 3.7 angstrom resolution map that was obtained in only 80 min on a desktop computer. These on-the-fly methods can be employed as an assessment of data quality from small samples and extended to high-throughput approaches.

  • 3.
    Kimanius, Dari
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Forsberg, Björn O.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Scheres, Sjors H. W.
    Lindahl, Erik
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab). KTH Royal Institute of Technology, Sweden.
    Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-22016In: eLIFE, E-ISSN 2050-084X, Vol. 5, e18722Article in journal (Refereed)
    Abstract [en]

    By reaching near-atomic resolution for a wide range of specimens, single-particle cryo-EM structure determination is transforming structural biology. However, the necessary calculations come at large computational costs, which has introduced a bottleneck that is currently limiting throughput and the development of new methods. Here, we present an implementation of the RELION image processing software that uses graphics processors (GPUs) to address the most computationally intensive steps of its cryo-EM structure determination workflow. Both image classification and high-resolution refinement have been accelerated more than an order-of-magnitude, and template-based particle selection has been accelerated well over two orders-of-magnitude on desktop hardware. Memory requirements on GPUs have been reduced to fit widely available hardware, and we show that the use of single precision arithmetic does not adversely affect results. This enables high-resolution cryo-EM structure determination in a matter of days on a single workstation.

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