Atomistic three-dimensional coherent x-ray imaging of nonbiological systems

Abstract

We computationally study the resolution limits for three-dimensional coherent x-ray diffractive imaging of heavy, nonbiological systems using Ar clusters as a prototype. We treat electronic and nuclear dynamics on an equal footing and remove the frozen-lattice approximation often used in electronic damage studies. We explore the achievable resolution as a function of pulse parameters (fluence level, pulse duration, and photon energy) and particle size. The contribution of combined lattice and electron dynamics is not negligible even for 2 fs pulses, and the Compton scattering is less deleterious than in biological systems for atomic-scale imaging. Although free-electron scattering represents a significant background, we find that recovery of the original structure is in principle possible with 3Å resolution for particles of 11 nm diameter.

The role of transient resonances for ultra-fast imaging of single sucrose nanoclusters

“…Monte-Carlo/Molecular-Dynamics calculations. To understand the scattering response of the sucrose clusters, or more generally organic nanoscale samples, we employed Monte-Carlo/Molecular-Dynamics (MC/MD) calculations 29,36 on Mira, a BG/Q supercomputer at the Argonne Leadership Computing Facility (see Methods IV C). In our model the interaction of the XFEL pulse with the cluster is treated quantum mechanically, all particles are propagated in time, and the time-dependent form factor including the delocalized electrons of the succrose clusters are calculated.…”

“…Further, the inner-shell absorption of intense x-ray pulses is a sequential process and for pulse durations comparable to the inner-shell lifetime, atoms 16 and clusters 20 can become transiently x-ray transparent. However, the effect of pulse duration under real imaging conditions has so far mostly been characterized in the hard x-ray regime 30,31,36 , but not in the water window or more generally near absorption edges where resonances play an important role at high x-ray intensities. For experimentalists it can be tempting to choose higher pulse energies over shorter pulse durations.…”

“…Monte-Carlo/Molecular-Dynamics Method. To understand the scattering response of the sucrose clusters, or more generally organic nanoscale samples, we employed Monte-Carlo/Molecular-Dynamics (MC/MD) calculations 29,36 to model the full electron and nuclear dynamics in an atomistic manner and calculate the resulting scattering patterns in parallel during the full duration of the x-ray pulse and under realistic beam parameters. The MC/MD approach is similar to the XMDYN method 51 .…”

Violation of centrosymmetry in time-resolved coherent x-ray diffraction from rovibrational states of diatomic molecules

“…Finally, the time-resolved transition amplitude T f i can be calculated by substituting Eqs. (16), (19) and (23) into Eq. (5).…”

“…Consequently, various aspects of x-ray physics and chemistry have been explored with these new x-ray sources [10,11]. For example, following ionization by intense x-rays, the ensuing dynamics in atoms [12][13][14], molecules [15][16][17], and clusters [18,19] have been studied. In this regard, absorption [20,21], stimulated emission [22][23][24], and photoelectron [25][26][27] spectroscopies have been shown to provide element-specific probes for studying these electronic and structural dynamics.…”