Brownian-motion based simulation of stochastic reaction–diffusion systems for affinity based sensors. (4th March 2016)

• Record Type: Journal Article
• Authors: Tulzer, Gerhard; Heitzinger, Clemens
• Is Part Of: Nanotechnology. Volume 27:Number 16(2016)
• Publication Date: 2016-03-04
• Subjects: fluctuations -- nanowire biosensors -- simulation; Nanotechnology -- Periodicals; Nanotechnology -- Periodicals; Nanotechnology; Publications périodiques; Nanotechnologies; Periodicals; 620.5
• DOI: 10.1088/0957-4484/27/16/165501
• Languages: English
• ISSNs: 0957-4484

Abstract

Abstract: In this work, we develop a 2D algorithm for stochastic reaction–diffusion systems describing the binding and unbinding of target molecules at the surfaces of affinity-based sensors. In particular, we simulate the detection of DNA oligomers using silicon-nanowire field-effect biosensors. Since these devices are uniform along the nanowire, two dimensions are sufficient to capture the kinetic effects features. The model combines a stochastic ordinary differential equation for the binding and unbinding of target molecules as well as a diffusion equation for their transport in the liquid. A Brownian-motion based algorithm simulates the diffusion process, which is linked to a stochastic-simulation algorithm for association at and dissociation from the surface. The simulation data show that the shape of the cross section of the sensor yields areas with significantly different target-molecule coverage. Different initial conditions are investigated as well in order to aid rational sensor design. A comparison of the association/hybridization behavior for different receptor densities allows optimization of the functionalization setup depending on the target-molecule density.