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The effect of electron-ion coupling on radiation damage simulations of a pyrochlore waste form

Crozier, Paul C.; Ismail, Ahmed I.; Foiles, Stephen M.

We have performed molecular dynamics simulations of cascade damage in the gadolinium pyrochlore Gd{sub 2}Zr{sub 2}O{sub 7}, comparing results obtained from traditional methodologies that ignore the effect of electron-ion interactions with a 'two-temperature model' in which the electronic subsystem is modeled using a diffusion equation to determine the electronic temperature. We find that the electron-ion interaction friction coefficient {gamma}{sub p} is a significant parameter in determining the behavior of the system following the formation of the primary knock-on atom (here, a U{sup 3+} ion). The mean final U{sup 3+} displacement and the number of defect atoms formed is shown to decrease uniformly with increasing {gamma}{sub p}; however, other properties, such as the final equilibrium temperature and the oxygen-oxygen radial distribution function show a more complicated dependence on {gamma}{sub p}.

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Structure and dynamics of water near the interface with oligo(ethylene oxide) self-assembled monolayers

Langmuir

Ismail, Ahmed I.; Grest, Gary S.; Stevens, Mark J.

We performed molecular dynamics simulations of the oligo(ethylene oxide) (OEO) self-assembled monolayers in water to determine the nature of the systems' interfacial structure and dynamics. The density profiles, hydrogen bonding, and water dynamics are calculated as a function of the area per molecule A of OEO. At the highest coverages, the interface is hydrophobic, and a density drop is found at the interface. The interfacial region becomes more like bulk water as A increases. The OEO and water become progressively more mixed, and hydrogen bonding increases within the interfacial region. Water mobility is slower within the interfacial region, but not substantially. The implications of our results on the resistance of OEO SAMs to protein adsorption are discussed. Our principal result is that as A increases the increasingly waterlike interfacial region provides a more protein-resistant surface. This finding supports recent experimental measurements that protein resistance is maximal for less than full coverage on Au. © 2007 American Chemical Society.

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Substructured multibody molecular dynamics

Crozier, Paul C.; Grest, Gary S.; Ismail, Ahmed I.; Lehoucq, Richard B.; Plimpton, Steven J.; Stevens, Mark J.

We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.

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16 Results
16 Results