Model for the dynamics of a water cluster in an x-ray free electron laser beam

Journal Article · Mon Nov 01 00:00:00 EST 2004 · Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics

DOI:https://doi.org/10.1103/PhysRevE.70.051904· OSTI ID:20636856

Bergh, Magnus; Timneanu, Nicusor; Spoel, David van der ^[1]

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1. Department of Cell and Molecular Biology, Biomedical Centre, Box 596, Uppsala University, S-75124 Uppsala (Sweden)

A microscopic sample placed into a focused x-ray free electron laser beam will explode due to strong ionization on a femtosecond time scale. The dynamics of this Coulomb explosion has been modeled by Neutze et al. [Nature (London) 406, 752 (2000)] for a protein, using computer simulations. The results suggest that by using ultrashort exposures, structural information may be collected before the sample is destroyed due to radiation damage. In this paper a method is presented to include the effect of screening by free electrons in the sample in a molecular dynamics simulation. The electrons are approximated by a classical gas, and the electron distribution is calculated iteratively from the Poisson-Boltzmann equation. Test simulations of water clusters reveal the details of the explosion dynamics, as well as the evolution of the free electron gas during the beam exposure. We find that inclusion of the electron gas in the model slows down the Coulomb explosion. The hydrogen atoms leave the sample faster than the oxygen atoms, leading to a double layer of positive ions. A considerable electron density is located between these two layers. The fact that the hydrogens are found to explode much faster than the oxygens means that the diffracting part of the sample stays intact somewhat longer than the sample as a whole.

• OSTI ID: 20636856
• Journal Information: Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, Vol. 70, Issue 5; Other Information: DOI: 10.1103/PhysRevE.70.051904; (c) 2004 The American Physical Society; Country of input: International Atomic Energy Agency (IAEA); ISSN 1063-651X
• Country of Publication: United States
• Language: English

Related Subjects

71 CLASSICAL AND QUANTUM MECHANICS
GENERAL PHYSICS
BOLTZMANN EQUATION
CATIONS
COMPUTERIZED SIMULATION
ELECTRON DENSITY
ELECTRON GAS
ELECTRONS
EVOLUTION
EXPLOSIONS
FREE ELECTRON LASERS
HYDROGEN
ITERATIVE METHODS
MOLECULAR CLUSTERS
MOLECULAR DYNAMICS METHOD
OXYGEN
PHOTOIONIZATION
POISSON EQUATION
PROTEINS
WATER
X RADIATION