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Density functional theory-based calculations of the (10,0) zigzag single-walled carbon nanotube with hydrogen chemisorbed exohedrally show that electron pairing and strain minimization lead hydrogen atoms to cluster and preferentially sit in axial configur ...
We present a new computational tool, METAGUI, which extends the VMD program with a graphical user interface that allows constructing a thermodynamic and kinetic model of a given process simulated by large-scale molecular dynamics. The tool is specially des ...
Starting from a disordered aggregate, we have simulated the formation of ordered amyloid-like beta structures in a system formed by 18 polyvaline chains in explicit solvent, employing molecular dynamics accelerated by bias-exchange metadynamics. We exploit ...
An important step in the computer simulation of the dynamics of biomolecules is the comparison of structures in a trajectory by exploiting a measure of distance. This allows distinguishing structures which are geometrically similar from those which are dif ...
Social permutation invariant coordinates are introduced describing the bond network around a given atom. They originate from the largest eigenvalue and the corresponding eigenvector of the contact matrix, are invariant under permutation of identical atoms, ...
We study dynamical processes at CdTe surfaces using ab initio metadynamics simulations. The c(2X2) to (2X1) transition of the Te-terminated (001) surface is found to involve a "c(2X2) + (2X1)" intermediate, consistent with experiment, and crossing of simil ...