An algorithm for three-dimensional Monte-Carlo simulation of charge distribution at biofunctionalized surfaces
| Autor: | Clemens Heitzinger, Alena Bulyha |
|---|---|
| Rok vydání: | 2011 |
| Předmět: |
Materials science
Surface Properties Static Electricity Monte Carlo method Nanowire 02 engineering and technology 010402 general chemistry 01 natural sciences Biopolymers Computer Simulation General Materials Science Boundary value problem chemistry.chemical_classification Models Statistical Biomolecule Charge density Charge (physics) 021001 nanoscience & nanotechnology 0104 chemical sciences Boundary layer Models Chemical chemistry 0210 nano-technology Biosensor Algorithm Algorithms |
| Zdroj: | Nanoscale. 3:1608 |
| ISSN: | 2040-3372 2040-3364 |
| DOI: | 10.1039/c0nr00791a |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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