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- Guio, P., et al.
(författare)
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Phase space vortices in collision-less plasmas
- 2003
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Ingår i: Nonlinear processes in geophysics. - 1023-5809 .- 1607-7946. ; 10:1/2, s. 75-86
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Tidskriftsartikel (refereegranskat)abstract
- Results on the formation and propagation of electron phase space vortices from laboratory experiments are summarized. The electron phase space vortices were excited in a strongly magnetized Q-machine plasma by applying a pulse to a segment of a waveguide surrounding the plasma. Depending on the temporal variation of the applied pulse, one or more phase space vortices can be excited, and their interaction can be followed in space and time. We were able to demonstrate, for instance, an irreversible coalescence of two such vortices. These results are extended by numerical simulations, showing how electron phase space vortices can also be formed by beam instabilities. Furthermore, a study of ion phase space vortices is performed by numerical simulations. Both codes allow for an externally applied magnetic field in three spatial dimensions. Ion phase space vortices are formed by the nonlinear saturation of the ion-ion two-stream instability, excited by injecting an ion beam at the plasma boundary. By following the evolution of the ion distribution of the velocity perpendicular to the direction of propagation of the injected ion beam, we find a significant ion heating in the direction perpendicular to the magnetic field associated with the ion phase space vortices being formed. The results are relevant, for instance, for the interpretation of observations by instrumented spacecraft in the Earth's ionosphere and magnetosphere.
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- Olsen, L, et al.
(författare)
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Binding of benzylpenicillin to metallo-beta-lactamase: A QM/MM study
- 2004
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Ingår i: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 108:45, s. 17639-17648
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Tidskriftsartikel (refereegranskat)abstract
- Metallo-beta-lactamases are bacterial enzymes that may function with either one or two zinc ions bound in the active site. In this work, the binding of benzylpenicillin to mono-zinc metallo-beta-lactamase from Bacillus cereus has been investigated in a docking procedure applying a combined quantum mechanical/molecular mechanical method as the final step. It is demonstrated that the substrate can bind with the carbonyl oxygen of the lactam ring coordinating to the zinc ion, and with the zinc-bound hydroxide ion in position for a nucleophilic attack on the carbonyl carbon of the lactam ring. In some structures, both the histidine and the cysteine at the other (unoccupied) metal-binding site are in a proper position to function as proton shuttles in proton transfer from the previously zinc-bound hydroxide, to the nitrogen in the lactam ring. In addition, the hydrophobic region formed by Phe34, Val39, Trp59, and Ala89 interacts with the phenyl group of benzylpenicillin, whereas the carboxylate group may be stabilized by Lys171 and Asn180. Alternatively, the carboxylate can bind to the zinc ion, prohibiting the nucleophilic attack of the zinc-bound hydroxide on the lactam carbonyl carbon. However, such a structure is energetically disfavored compared to the other enzyme-substrate complexes.
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