Secondary Electron Cascade Dynamics in KI and CsI

Ortiz, Carlos; Caleman, Carl

doi:10.1021/jp0736692

Cited by 10 publications

(11 citation statements)

References 58 publications

(100 reference statements)

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“…[9][10][11] In the near future, hard X-ray sources like X-ray free electron lasers (XFEL), such as the Linac coherent light source (LCLS) 12 in Menlo Park, California and the European XFEL 13 in Hamburg, as well as table-top XFELs, [14][15][16][17][18] will provide X-ray pulses that allow imaging of single molecules 19 or even entire living cells 20 at, or near, atomic resolution. Due to the severe radiation damage by photo ionizations 19,21,22 and subsequent impact ionizations [23][24][25][26] induced by the intense X-ray pulses, every sample will diffract only once. To get enough useful signal scattered onto the detector, samples must be delivered into the X-ray beam in a repetitive and reliable manner; 27 ESI methods have proven to be capable of just that.…”

Section: Introductionmentioning

confidence: 99%

Structural stability of electrosprayed proteins: temperature and hydration effects

Marklund

Larsson

Spoel

et al. 2009

Phys. Chem. Chem. Phys.

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Electrospray ionization is a gentle method for sample delivery, routinely used in gas-phase studies of proteins. It is crucial for structural investigations that the protein structure is preserved, and a good understanding of how structure is affected by the transition to the gas phase is needed for the tuning of experiments to meet that requirement. Small amounts of residual solvent have been shown to protect the protein, but temperature is important too, although it is not well understood how the latter affects structural details. Using molecular dynamics we have simulated four sparingly hydrated globular proteins (Trp-cage; Ctf, a C-terminal fragment of a bacterial ribosomal protein; ubiquitin; and lysozyme) in vacuum starting at temperatures ranging from 225 K to 425 K. For three of the proteins, our simulations show that a water layer corresponding to 3 A preserves the protein structure in vacuum, up to starting temperatures of 425 K. Only Ctf shows minor secondary structural changes at lower starting temperatures. The structural conservation stems mainly from interactions with the surrounding water. Temperature scales in simulations are not directly translatable into experiments, but the wide temperature range in which we find the proteins to be stable is reassuring for the success of future single particle imaging experiments. The water molecules aggregate in clusters and form patterns on the protein surface, maintaining a reproducible hydrogen bonding network. The simulations were performed mainly using OPLS-AA/L, with cross checks using AMBER03 and GROMOS96 53a6. Only minor differences between the results from the three different force fields were observed.

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Section: Introductionmentioning

confidence: 99%

Structural stability of electrosprayed proteins: temperature and hydration effects

Marklund

Larsson

Spoel

et al. 2009

Phys. Chem. Chem. Phys.

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“…Thus, urea crystals are a good model for protein nanocrystals, known to contain 30%-60% water. We refer to [5,9,16] and the supplementary material for further details of these calculations and how the model compares with experiments on diamond [17]. Considering m i to be the mass of electron i and r i the position of electron i with respect to the center of mass of all free electrons, the radius of gyration, used in Figure 2, is defined as…”

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confidence: 99%

On the Feasibility of Nanocrystal Imaging Using Intense and Ultrashort X-ray Pulses

et al. 2010

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Structural studies of biological macromolecules are severely limited by radiation damage. Traditional crystallography curbs the effects of damage by spreading damage over many copies of the molecule of interest in the crystal. X-ray lasers offer an additional opportunity for limiting damage by out-running damage processes with ultrashort and very intense X-ray pulses. Such pulses may allow the imaging of single molecules, clusters, or nanoparticles. Coherent flash imaging will also open up new avenues for structural studies on nano- and microcrystalline substances. This paper addresses the theoretical potentials and limitations of nanocrystallography with extremely intense coherent X-ray pulses. We use urea nanocrystals as a model for generic biological substances and simulate the primary and secondary ionization dynamics in the crystalline sample. The results establish conditions for ultrafast single-shot nanocrystallography diffraction experiments as a function of X-ray fluence, pulse duration, and the size of nanocrystals. Nanocrystallography using ultrafast X-ray pulses has the potential to open up a new route in protein crystallography to solve atomic structures of many systems that remain inaccessible using conventional X-ray sources.

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“…Non-thermal melting can be caused by absorption of multiple photons from, for instance, a Ti : sapphire laser, which leads to direct as well as indirect ionization processes (through secondary electron cascades [19][20][21][22][23][24][25]. Quite a few studies of the different mechanisms leading to thermal and non-thermal melting of silicon and other semiconductors have been presented recently, [26][27][28][29][30][31] and similar studies for metals have been reported as well.…”

Section: Introductionmentioning

confidence: 92%

Structural studies of melting on the picosecond time scale

Spoel

Maia

Caleman

2008

Phys. Chem. Chem. Phys.

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Ultrafast structural studies of laser-induced melting have demonstrated that the solid-liquid phase transition can take place on a picosecond time scale in a variety of materials. Experimental studies using ångström wavelength X-rays from the sub-picosecond pulse source at Stanford (now retired) on non-thermal melting of semi-conductors, such as indium antimonide, employed the decay of a single Bragg-peak to measure the time component of the phase transition. These materials were found to start melting within one picosecond after the laser pulse. Recent computer simulations have described the thermal melting of ice induced by an infrared laser pulse. Here it was shown that melting can happen within a few picoseconds, somewhat slower than non-thermal melting in semi-conductors. These computer simulations are compatible with spectroscopy experiments on ice-melting, demonstrating that simulations form a very powerful complement to experiments targeting the process of phase-transitions. Here we present an overview of recent experimental and theoretical studies of melting, as well as new simulations of ice-melting where the effect of the size of the crystal on scattering is studied. Based on simulations of a near-macroscopic crystal, we predict the decay of the most intense Bragg peaks of ice following heating by laser pulse, by modeling the scattering from the melting sample in the simulations.

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Secondary Electron Cascade Dynamics in KI and CsI

Cited by 10 publications

References 58 publications

Structural stability of electrosprayed proteins: temperature and hydration effects

Structural stability of electrosprayed proteins: temperature and hydration effects

On the Feasibility of Nanocrystal Imaging Using Intense and Ultrashort X-ray Pulses

Structural studies of melting on the picosecond time scale

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