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Packing structures of single-stranded DNA and double-stranded DNA thiolates on Au(111): A molecular simulation study
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10.1063/1.2786984
/content/aip/journal/jcp/127/19/10.1063/1.2786984
http://aip.metastore.ingenta.com/content/aip/journal/jcp/127/19/10.1063/1.2786984

Figures

Image of FIG. 1.
FIG. 1.

A hexagonal lattice structure and its repeating structure.

Image of FIG. 2.
FIG. 2.

(Color online) Illustrations of three of the unit cells that were used for simulations with surface packing areas of 4.1, 7.9, and /DNA chain, respectively. These simulation cells have the same volume and the same type and number of molecules. Their total energies are compared to determine optimal packing structure.

Image of FIG. 3.
FIG. 3.

The total potential energy at different surface packing areas for ssDNA in a hexagonal lattice structure and NaCl solution at calculated from simulations. The error bars represent the standard deviation of the potential energy over the last of the simulation, which reflects the thermal fluctuation of the energy of the system in the sampled configuration.

Image of FIG. 4.
FIG. 4.

The total potential energy at different surface packing areas for ssDNA in a hexagonal lattice structure without extra ions at calculated from simulations. The error bars are defined in the caption of Fig. 3.

Image of FIG. 5.
FIG. 5.

The total potential energy at different surface packing areas for dsDNA in a hexagonal lattice structure and NaCl solution at calculated from simulations. The error bars are defined in the caption of Fig. 3.

Image of FIG. 6.
FIG. 6.

(Color online) Snapshots of ssDNA(a) and dsDNA(b) at three time points (, , and ) during MD simulations.

Tables

Generic image for table
Table I.

Lattice parameters for hexagonal lattice structures with various surface packing areas used in ssDNA simulations.

Generic image for table
Table II.

Lattice parameters for hexagonal lattice structures with various surface packing areas used in dsDNA simulations.

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/content/aip/journal/jcp/127/19/10.1063/1.2786984
2007-11-15
2014-04-25
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Packing structures of single-stranded DNA and double-stranded DNA thiolates on Au(111): A molecular simulation study
http://aip.metastore.ingenta.com/content/aip/journal/jcp/127/19/10.1063/1.2786984
10.1063/1.2786984
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