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

Alena Bulyha, Clemens Heitzinger

Research output: Contribution to journalArticle

19 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)1608-1617
Number of pages10
JournalNanoscale
Volume3
Issue number4
DOIs
StatePublished - Apr 2011
Externally publishedYes

Fingerprint

Charge distribution
Biomolecules
Radiation counters
Nanowires
Screening
Boundary layers
Molecules
Electric potential
Sodium chloride
Biosensors
Sodium Chloride
Electrolytes
Transducers
Monte Carlo simulation
Statistics
Boundary conditions
Sensors
Experiments

ASJC Scopus subject areas

  • Materials Science(all)

Cite this

An algorithm for three-dimensional Monte-Carlo simulation of charge distribution at biofunctionalized surfaces. / Bulyha, Alena; Heitzinger, Clemens.

In: Nanoscale, Vol. 3, No. 4, 04.2011, p. 1608-1617.

Research output: Contribution to journalArticle

Bulyha, Alena ; Heitzinger, Clemens. / An algorithm for three-dimensional Monte-Carlo simulation of charge distribution at biofunctionalized surfaces. In: Nanoscale. 2011 ; Vol. 3, No. 4. pp. 1608-1617.
@article{0041e68089bb421fa6258ba7c17884ef,
title = "An algorithm for three-dimensional Monte-Carlo simulation of charge distribution at biofunctionalized surfaces",
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.",
author = "Alena Bulyha and Clemens Heitzinger",
year = "2011",
month = "4",
doi = "10.1039/c0nr00791a",
language = "English (US)",
volume = "3",
pages = "1608--1617",
journal = "Nanoscale",
issn = "2040-3364",
publisher = "Royal Society of Chemistry",
number = "4",

}

TY - JOUR

T1 - An algorithm for three-dimensional Monte-Carlo simulation of charge distribution at biofunctionalized surfaces

AU - Bulyha, Alena

AU - Heitzinger, Clemens

PY - 2011/4

Y1 - 2011/4

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=79953764902&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=79953764902&partnerID=8YFLogxK

U2 - 10.1039/c0nr00791a

DO - 10.1039/c0nr00791a

M3 - Article

C2 - 21301731

AN - SCOPUS:79953764902

VL - 3

SP - 1608

EP - 1617

JO - Nanoscale

JF - Nanoscale

SN - 2040-3364

IS - 4

ER -