Brownian-motion based simulation of stochastic reaction-diffusion systems for affinity based sensors

• Published in: Nanotechnology Vol. 27; no. 16; pp. 165501 - 165509
• Main Authors: Tulzer, Gerhard, Heitzinger, Clemens
• Format: Journal Article
• Language: English
• Published: England IOP Publishing 22.04.2016
• Subjects: Algorithms; Binding; Computer simulation; Diffusion; fluctuations; Mathematical models; nanowire biosensors; Sensors; simulation; Stochasticity; Two dimensional
• ISSN: 0957-4484; 1361-6528; 1361-6528
• DOI: 10.1088/0957-4484/27/16/165501

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.