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

Handle URI:
http://hdl.handle.net/10754/597507
Title:
An algorithm for three-dimensional Monte-Carlo simulation of charge distribution at biofunctionalized surfaces
Authors:
Bulyha, Alena; Heitzinger, Clemens
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.
Publisher:
Royal Society of Chemistry (RSC)
Journal:
Nanoscale
KAUST Grant Number:
KUK-I1-007-43
Issue Date:
2011
DOI:
10.1039/c0nr00791a
PubMed ID:
21301731
Type:
Article
ISSN:
2040-3364; 2040-3372
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).
Appears in Collections:
Publications Acknowledging KAUST Support

Full metadata record

DC FieldValue Language
dc.contributor.authorBulyha, Alenaen
dc.contributor.authorHeitzinger, Clemensen
dc.date.accessioned2016-02-25T12:41:05Zen
dc.date.available2016-02-25T12:41:05Zen
dc.date.issued2011en
dc.identifier.citationBulyha 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.en
dc.identifier.issn2040-3364en
dc.identifier.issn2040-3372en
dc.identifier.pmid21301731en
dc.identifier.doi10.1039/c0nr00791aen
dc.identifier.urihttp://hdl.handle.net/10754/597507en
dc.description.abstractIn 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.en
dc.description.sponsorshipThis 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).en
dc.publisherRoyal Society of Chemistry (RSC)en
dc.titleAn algorithm for three-dimensional Monte-Carlo simulation of charge distribution at biofunctionalized surfacesen
dc.typeArticleen
dc.identifier.journalNanoscaleen
dc.contributor.institutionUniversitat Wien, Vienna, Austriaen
dc.contributor.institutionUniversity of Cambridge, Cambridge, United Kingdomen
kaust.grant.numberKUK-I1-007-43en
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