| 1. |
- Ahlberg Gagnér, Viktor, 1989, et al.
(author)
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Clustering of atomic displacement parameters in bovine trypsin reveals a distributed lattice of atoms with shared chemical properties
- 2019
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In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322 .- 2045-2322. ; 9:1
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Journal article (peer-reviewed)abstract
- Low-frequency vibrations are crucial for protein structure and function, but only a few experimental techniques can shine light on them. The main challenge when addressing protein dynamics in the terahertz domain is the ubiquitous water that exhibit strong absorption. In this paper, we observe the protein atoms directly using X-ray crystallography in bovine trypsin at 100 K while irradiating the crystals with 0.5 THz radiation alternating on and off states. We observed that the anisotropy of atomic displacements increased upon terahertz irradiation. Atomic displacement similarities developed between chemically related atoms and between atoms of the catalytic machinery. This pattern likely arises from delocalized polar vibrational modes rather than delocalized elastic deformations or rigid-body displacements. The displacement correlation between these atoms were detected by a hierarchical clustering method, which can assist the analysis of other ultra-high resolution crystal structures. These experimental and analytical tools provide a detailed description of protein dynamics to complement the structural information from static diffraction experiments. © 2019, The Author(s).
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| 2. |
- Andersson, Jonas, et al.
(author)
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Parametrization of energy sharing distributions in direct double photoionization of He
- 2019
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In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9
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Journal article (peer-reviewed)abstract
- We present experimental results on the characteristic sharing of available excess energy, ranging from 11–221eV, between two electrons in single-photon direct double ionization of He. An effective parametrization of the sharing distributions is presented along with an empirical model that describes the complete shape of the distribution based on a single experimentally determinable parameter. The measured total energy sharing distributions are separated into two distributions representing the shake-off and knock-out parts by simulating the sharing distribution curves expected from a pure wave collapse after a sudden removal of the primary electron. In this way, empirical knock-out distributions are extracted and both the shake-off and knock-out distributions are parametrized. These results suggest a simple method that can be applied to other atomic and molecular systems to experimentally study important aspects of the direct double ionization process.
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| 3. |
- Chulkov, Ruslan, 1972-, et al.
(author)
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Effects of emittance and energy spread in an electron bunch on THz radiation generated by a super-radiant source : report III of the series of reports by the Swedish FEL Center and FREIA Group
- 2014
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Reports (other academic/artistic)abstract
- In this report we summarize our results on simulation of a super-radiant sourceoperating at the THz spectral range. We consider an open-type undulator com-prising plane magnets but without any guiding structure for generated THz eld.The undulator is assumed to be driven by electron bunches of femtosecond durationwhich are produced by an rf Linac. Using a numerical model developed, we analyzeeects of the bunch parameters on output performance of the super-radiant sourceand reveal some surprising results. Specically, we show that degradation in bunchspatial quality (increase in the bunch emittance) should lead to decrease in angulardivergence and spectral narrowing of the THz radiation. We also demonstrate thatelectron energy spread which commonly leads to bunch broadening and radiativeenergy drop can be eventually suppressed under appropriate conditions.
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| 4. |
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| 5. |
- Jensen, Maja, 1978, et al.
(author)
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High-resolution macromolecular crystallography at the FemtoMAX beamline with time-over-threshold photon detection
- 2021
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In: Journal of Synchrotron Radiation. - 1600-5775 .- 0909-0495. ; 28, s. 64-70
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Journal article (peer-reviewed)abstract
- Protein dynamics contribute to protein function on different time scales. Ultrafast X-ray diffraction snapshots can visualize the location and amplitude of atom displacements after perturbation. Since amplitudes of ultrafast motions are small, high-quality X-ray diffraction data is necessary for detection. Diffraction from bovine trypsin crystals using single femtosecond X-ray pulses was recorded at FemtoMAX, which is a versatile beamline of the MAX IV synchrotron. The time-over-threshold detection made it possible that single photons are distinguishable even under short-pulse low-repetition-rate conditions. The diffraction data quality from FemtoMAX beamline enables atomic resolution investigation of protein structures. This evaluation is based on the shape of the Wilson plot, cumulative intensity distribution compared with theoretical distribution, I/σ, Rmerge /Rmeas and CC1/2 statistics versus resolution. The FemtoMAX beamline provides an interesting alternative to X-ray free-electron lasers when studying reversible processes in protein crystals.
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| 6. |
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| 7. |
- Opanasenko, Anatoliy, 1961-, et al.
(author)
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Towards a combined THz/X-ray source : report IV of the series of reports by the Swedish FEL Center and the FREIA Group
- 2014
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Reports (other academic/artistic)abstract
- In the framework of development of a Free Electron Laser (FEL) by the Swedish FEL Center and theFREIA laboratory, we discuss the design of a versatile combined THz/X-ray source driven by high-brightness electron bunches produced by a superconducting linear accelerator. The ultimate goal isto build a versatile photon source for multidisciplinary research at the FREIA laboratory of UppsalaUniversity. A signicant part of equipment is potentially available via the FREIA project at UppsalaUniversity after 2018 such as the cryogenic system, the system of power generation and transportation,control and data acquisition systems. For pump-probe experiments, we discus a possibility to combinethe THz source with an X-ray source based on the inverse Compton scattering of quantum laser pulsesfrom electron bunches. The X-ray source will operate in the \water window" with an output intensitycomparable to a second generation synchrotron. The envisioned THz/X-ray source is compact andcomparable in budget to the cost of one beamline at MAX IV. The source can also be used to trainstudents in accelerator physics and applications of THz and synchrotron radiation.
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| 8. |
- Zhaunerchyk, Vitali, 1981-
(author)
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Dynamics in the Dissociative Recombination of Small Polyatomic Molecular Ions
- 2008
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Doctoral thesis (other academic/artistic)abstract
- Dissociative recombination (DR) is a process in which a positive molecular ion recombines with an electron and subsequently dissociates into neutral fragments. Among the different types of molecular ion-electron reactions DR deserves particular attention due to the important role it plays in low-temperature and low-density plasmas. Despite the apparent simplicity of the DR reaction, its investigation has proven to be a difficult task from both experimental and theoretical perspectives. In order to shed more light upon this process the storage ring technique has been introduced and utilised extensively for the last few decades. This thesis is devoted to experimental studies into the DR reaction at the storage ring CRYRING. The DR reaction has been investigated for the following molecular ions; Na+(D2O), PD2+, O3+, N3+, H2+, D2H+, OPCl+, OPCl2+ and H3O+, with the aim to ascertain rotational state effects, to find patterns in the branching products of similar molecular ions, to investigate isotope effects and to study in detail the dynamics involved in the three-body break-up channel.
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