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    An algorithm for three-dimensional Monte-Carlo simulation of charge distribution at biofunctionalized surfaces

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    Type
    Article
    Authors
    Bulyha, Alena
    Heitzinger, Clemens
    KAUST Grant Number
    KUK-I1-007-43
    Date
    2011
    Permanent link to this record
    http://hdl.handle.net/10754/597507
    
    Metadata
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    Abstract
    In this work, a Monte-Carlo algorithm in the constant-voltage ensemble for the calculation of 3d charge concentrations at charged surfaces functionalized with biomolecules is presented. The motivation for this work is the theoretical understanding of biofunctionalized surfaces in nanowire field-effect biosensors (BioFETs). This work provides the simulation capability for the boundary layer that is crucial in the detection mechanism of these sensors; slight changes in the charge concentration in the boundary layer upon binding of analyte molecules modulate the conductance of nanowire transducers. The simulation of biofunctionalized surfaces poses special requirements on the Monte-Carlo simulations and these are addressed by the algorithm. The constant-voltage ensemble enables us to include the right boundary conditions; the dna strands can be rotated with respect to the surface; and several molecules can be placed in a single simulation box to achieve good statistics in the case of low ionic concentrations relevant in experiments. Simulation results are presented for the leading example of surfaces functionalized with pna and with single- and double-stranded dna in a sodium-chloride electrolyte. These quantitative results make it possible to quantify the screening of the biomolecule charge due to the counter-ions around the biomolecules and the electrical double layer. The resulting concentration profiles show a three-layer structure and non-trivial interactions between the electric double layer and the counter-ions. The numerical results are also important as a reference for the development of simpler screening models. © 2011 The Royal Society of Chemistry.
    Citation
    Bulyha A, Heitzinger C (2011) An algorithm for three-dimensional Monte-Carlo simulation of charge distribution at biofunctionalized surfaces. Nanoscale 3: 1608. Available: http://dx.doi.org/10.1039/c0nr00791a.
    Sponsors
    This work was supported by the FWF (Austrian Science Fund) project No. P20871-N13, by the WWTF (Viennese Science and Technology Fund) project No. MA09-028, and by the EU project DEASE (contract MEST-CT-2005-021122). This publication is based on work supported by Award No. KUK-I1-007-43, funded by the King Abdullah University of Science and Technology (KAUST).
    Publisher
    Royal Society of Chemistry (RSC)
    Journal
    Nanoscale
    DOI
    10.1039/c0nr00791a
    PubMed ID
    21301731
    ae974a485f413a2113503eed53cd6c53
    10.1039/c0nr00791a
    Scopus Count
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