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Molecular dynamics (MD) simulations continue to make important contributions to understanding chemical and physical processes. Concomitant with the growth of MD simulations is the need to have interaction potentials that both represent the chemistry of the system and are computationally efficient. We propose a modification to the ReaxFF potential for carbon and hydrogen that eliminates the time-consuming charge equilibration, eliminates the acknowledged flaws of the electronegativity equalization method, includes an expanded training set for condensed phases, has a repulsive wall for simulations of energetic particle bombardment, and is compatible with the LAMMPS code. This charge-implicit ReaxFF potential is five times faster than the conventional ReaxFF potential for a simulation of keV particle bombardment with a sample size of over 800 000 atoms.

Defects and morphological changes in nanothin Cu films on polycrystalline Mo analyzed by thermal helium desorption spectrometry Molecular dynamics computer simulations are employed to investigate the effect of projectile size and surface morphology on the angular emission stimulated by impact of Ar gas cluster projectiles. Argon clusters of sizes n ¼ 10-1000 and kinetic energies of 10 and 20 keV Ar n aimed at normal incidence are used to sputter Ag(100) and Mo(100) samples. The total sputtering yield is larger for Ag(100) than for Mo(100). The ratio of sputtering yields is inversely proportional to the ratio of sublimation energies of these solids for projectiles between Ar 20 and Ar 250 . In both systems, the angular distributions are sensitive to both the projectile size and the surface roughness. The maximum of angular spectra shifts from direction normal to the surface toward off-normal direction with the increase in the projectile size. An opposite trend is observed with the increase in the surface roughness. Formation of a cloud composed of projectile atoms and the enhanced lateral material relocation caused by projectile lateral expansion upon impact are the main factors responsible for promoting off-normal ejection. On the other hand, material ejection from randomly inclined surface areas and the influence of nearby topography are found to be responsible for enhancing ejection along the surface normal for rough surfaces.

Topography development is one of the main factors limiting the quality of depth profiles during depth profiling experiments. One possible source of topography development is the formation of self-organized patterns due to cluster ion beam irradiation. In this work, we propose a simple model that can intuitively explain this phenomenon in terms of impact-induced mass transfer. By coupling our model with molecular dynamics simulations, we can predict the critical incidence angle, which separates the smoothening and roughening regimes. The results are in quantitative agreement with experiments. It is observed that the problems arising from topography development during depth profiling with cluster projectiles can be mitigated by reducing the beam incidence angle with respect to the surface normal or increasing its kinetic energy.

Three-dimensional (3D) molecular imaging of biological structures is important for a wide range of research. In recent decades, secondary-ion mass spectrometry (SIMS) has been recognized as a powerful technique for both twodimensional and 3D molecular imaging. Sample fixations (e.g., chemical fixation and cryogenic fixation methods) are necessary to adapt biological samples to the vacuum condition in the SIMS chamber, which has been demonstrated to be nontrivial and less controllable, thus limiting the wider application of SIMS on 3D molecular analysis of biological samples. Our group recently developed in situ liquid SIMS that offers great opportunities for the molecular study of various liquids and liquid interfaces. In this work, we demonstrate that a further development of the vacuum-compatible microfluidic device used in in situ liquid SIMS provides a convenient freeze-fixation of biological samples and leads to more controllable and convenient 3D molecular imaging. The special design of this new vacuumcompatible liquid chamber allows an easy determination of sputter rates of ice, which is critical for calibrating the depth scale of frozen biological samples. Sputter yield of a 20 keV Ar 1800 + ion on ice has been determined as 1500 (±8%) water molecules per Ar 1800 + ion, consistent with our results from molecular dynamics simulations. Moreover, using the information of ice sputter yield, we successfully conduct 3D molecular imaging of frozen homogenized milk and observe network structures of interesting organic and inorganic species. Taken together, our results will significantly benefit various research fields relying on 3D molecular imaging of biological structures.