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Monte Carlo DNA Simulator
Simulate ionic concentration profiles at charged boundaries functionalized with DNA oligomers.
Launch Tool
Archive Version 1.0
Published on 08 Sep 2009 All versions
doi:10.4231/D3BZ6176M cite this
This tool is closed source.
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Abstract
The MCDNA tool calculates ionic (Na and Cl) concentration profiles in
electrolytes between two charged surfaces. A voltage difference
between the two electrodes can be applied and one of the electrodes
can be functionalized with different types of biomolecules. The
leading application are the surfaces of BioFETs (biologically
sensitive field-effect transistors). The simulations are
three-dimensional Metropolis Monte-Carlo calculations in the
constant-voltage ensemble.
One of the surfaces can be functionalized with PNA (peptide nucleic
acid), ssDNA (single-stranded DNA), or dsDNA (double-stranded DNA)
oligomers. In addition to the concentration profiles, other
quantities of interest such as the chemical potential, the surface
charge density, and the dipole moment density of the boundary layer at
the functionalized surface are calculated.
The whole system is electrically neutral and periodic in the two
coordinate directions of the parallel surfaces. The density of the
biomolecules at the surface can be adjusted via their distance. A
simulation box can contain several molecules, since otherwise the
number of ions in a simulation box would be too small for meaningful
calculations at low ionic concentrations.
If there is a single molecule in the simulation box, it is linked at
the center of the lower electrode. If the simulation box contains
more molecules, they are arranged in a square grid and each molecule
is centered in its grid cell. Each oligomer is bound to the surface
by a linker. The PNA and DNA oligomers and their linkers are modeled
as impenetrable cylinders with two hemispheres of the same radius at
the top and at the bottom. PNA oligomers are modeled by uncharged
cylinders, and ssDNA and dsDNA oligomers carry the charges of the
phosphate groups of the backbone on their outside just as in B-DNA
oligomers. The linkers are orthogonal to the surface so that they
touch the surface. The upper hemisphere of the linker overlaps with
the lower hemisphere of the oligomer and acts as a flexible joint.
Hence the oligomers can be rotated with respect to the surface.
The length of the linkers and the number of nucleotides in the
oligomers, the number of oligomers in the simulation box, the distance
between them, and their angle with respect to the surface plane are
parameters of the simulation. Furthermore, the ionic concentration
and the distance between the two electrodes must be specified. The
distance between the two electrodes, i.e., the height of simulation
box, and the applied voltage yield the electric field in the
simulation box.
The accuracy of the Monte-Carlo simulations is determined by the
algorithmic parameters. The default algorithmic parameters yield fast
results with relatively small noise.
Credits
The simulator is based on Monte-Carlo code provided by Prof. Dezső Boda (Department of Physical Chemistry, University of Pannonia).
Sponsored by
The development of this simulator has been supported by research projects funded by the Austrian Academy of Sciences (ÖAW) and the Austrian Science Fund (FWF).
Publications
Alena Bulyha, Clemens Heitzinger, and Norbert Mauser. Three-dimensional Monte Carlo simulation of biofunctionalized surface layers in the constant-voltage ensemble. Submitted for publication.
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