Applicability of the classical molecular dynamics method to study x-ray irradiated molecular systems

Jurek, Zoltán; Ziaja, Beata; Santra, Robin

doi:10.1088/0953-4075/47/12/124036

Cited by 15 publications

(13 citation statements)

References 25 publications

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“…XMDYN simulations follow the temporal evolution of a stochastically ionized system. The code has been successfully applied to describe the interaction of clusters and macromolecules with X-rays 31,32,53,54 . It is not computationally feasible to simulate the dynamics of a non-uniformly irradiated crystal with a size of a few hundred nm using a code that follows the trajectories of all atoms and electrons individually.…”

Section: Methodsmentioning

confidence: 99%

Structural dynamics in proteins induced by and probed with X-ray free-electron laser pulses

et al. 2020

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X-ray free-electron lasers (XFELs) enable crystallographic structure determination beyond the limitations imposed upon synchrotron measurements by radiation damage. The need for very short XFEL pulses is relieved through gating of Bragg diffraction by loss of crystalline order as damage progresses, but not if ionization events are spatially non-uniform due to underlying elemental distributions, as in biological samples. Indeed, correlated movements of iron and sulfur ions were observed in XFEL-irradiated ferredoxin microcrystals using unusually long pulses of 80 fs. Here, we report a femtosecond time-resolved X-ray pump/X-ray probe experiment on protein nanocrystals. We observe changes in the protein backbone and aromatic residues as well as disulfide bridges. Simulations show that the latter's correlated structural dynamics are much slower than expected for the predicted high atomic charge states due to significant impact of ion caging and plasma electron screening. This indicates that dense-environment effects can strongly affect local radiation damage-induced structural dynamics.

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Section: Methodsmentioning

confidence: 99%

Structural dynamics in proteins induced by and probed with X-ray free-electron laser pulses

et al. 2020

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“…XMDYN [20] is a versatile molecular dynamics simulation code for modeling matter irradiated by intense x-ray pulses. The approach has been validated against various experimental results [16,17,31]. The code follows the ionization dynamics of the individual atoms initiated by x-ray photons using the Monte Carlo method.…”

Section: Molecular Dynamics Code For Validating Hydrodynamic Simulationsmentioning

confidence: 99%

Hydrodynamic model for picosecond propagation of laser-created nanoplasmas

Saxena¹,

Jurek²,

Ziaja³

et al. 2015

High Energy Density Physics

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a b s t r a c tThe interaction of a free-electron-laser pulse with a moderate or large size cluster is known to create a quasi-neutral nanoplasma, which then expands on hydrodynamic timescale, i.e., > 1 ps. To have a better understanding of ion and electron data from experiments derived from laser-irradiated clusters, one needs to simulate cluster dynamics on such long timescales for which the molecular dynamics approach becomes inefficient. We therefore propose a two-step Molecular Dynamics-Hydrodynamic scheme. In the first step we use molecular dynamics code to follow the dynamics of an irradiated cluster until all the photo-excitation and corresponding relaxation processes are finished and a nanoplasma, consisting of ground-state ions and thermalized electrons, is formed. In the second step we perform long-timescale propagation of this nanoplasma with a computationally efficient hydrodynamic approach.In the present paper we examine the feasibility of a hydrodynamic two-fluid approach to follow the expansion of spherically symmetric nanoplasma, without accounting for the impact ionization and three-body recombination processes at this stage. We compare our results with the corresponding molecular dynamics simulations. We show that all relevant information about the nanoplasma propagation can be extracted from hydrodynamic simulations at a significantly lower computational cost when compared to a molecular dynamics approach. Finally, we comment on the accuracy and limitations of our present model and discuss possible future developments of the two-step strategy.

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“…In the latter case, a simulation method which follows individual realizations of the system (shot-to-shot) with correlations included intrinsically would be a more preferable choice. Molecular dynamics (MD) modeling is an example of such method [1,[43][44][45]. It also accounts for the granularity of ions.…”

Section: Effect Of Interparticle Correlationsmentioning

confidence: 99%

“…However, this is only an approximate treatment. Especially for low energy particles [45] quantum effects do play a role and cannot be treated accurately in such an approximate way. Therefore, we view the classical approximation as the main limitation of the MD approach.…”

Section: Effect Of Interparticle Correlationsmentioning

confidence: 99%

Towards Realistic Simulations of Macromolecules Irradiated under the Conditions of Coherent Diffraction Imaging with an X-ray Free-Electron Laser

et al. 2015

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Biological samples are highly radiation sensitive. The rapid progress of their radiation damage prevents accurate structure determination of single macromolecular assemblies in standard diffraction experiments. However, computer simulations of the damage formation have shown that the radiation tolerance might be extended at very high intensities with ultrafast imaging such as is possible with the presently developed and operating x-ray free-electron lasers. Recent experiments with free-electron lasers on nanocrystals have demonstrated proof of the imaging principle at resolutions down to 1.6 Angstroms. However, there are still many physical and technical problems to be clarified on the way to imaging of single biomolecules at atomic resolution. In particular, theoretical simulations try to address an important question: How does the radiation damage progressing within an imaged single object limit the structural information about this object recorded in its diffraction image during a 3D imaging experiment? This information is crucial for adjusting pulse parameters during imaging so that high-resolution diffraction patterns can be obtained. Further, dynamics simulations should be used to verify the accuracy of the structure reconstruction performed from the experimental data. This is an important issue as the experimentally recorded diffraction signal is recorded from radiation-damaged samples.

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Applicability of the classical molecular dynamics method to study x-ray irradiated molecular systems

Cited by 15 publications

References 25 publications

Structural dynamics in proteins induced by and probed with X-ray free-electron laser pulses

Structural dynamics in proteins induced by and probed with X-ray free-electron laser pulses

Hydrodynamic model for picosecond propagation of laser-created nanoplasmas

Towards Realistic Simulations of Macromolecules Irradiated under the Conditions of Coherent Diffraction Imaging with an X-ray Free-Electron Laser

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