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- Steven M. Swasey, Leonardo Espinosa Leal, Olga Lopez-Acevedo, James Pavlovich, Elisabeth G. Gwinn
- Scientific reports
- 2015

Metal ion interactions with DNA have far-reaching implications in biochemistry and DNA nanotechnology. Ag(+) is uniquely interesting because it binds exclusively to the bases rather than the backbone of DNA, without the toxicity of Hg(2+). In contrast to prior studies of Ag(+) incorporation into double-stranded DNA, we remove the constraints of Watson-Crick… (More)

We present a computational scheme for orbital-free density functional theory (OFDFT) that simultaneously provides access to all-electron values and preserves the OFDFT linear scaling as a function of the system size. Using the projector augmented-wave method (PAW) in combination with real-space methods, we overcome some obstacles faced by other available… (More)

Multi-scale computer simulations combine the computationally efficient classical algorithms with more expensive but also more accurate ab-initio quantum mechanical algorithms. This work describes one implementation of multi-scale computations using the Atomistic Simulation Environment (ASE). This implementation can mix classical codes like LAMMPS and the… (More)

A quantum walk, i.e., the quantum evolution of a particle on a graph, is termed scalar if the internal space of the moving particle (often called the coin) has dimension one. Here, we study the existence of scalar quantum walks on Cayley graphs, which are built from the generators of a group. After deriving a necessary condition on these generators for the… (More)

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