Integrating Molecular Dynamics for DNA Bio-Chip Fabrication and Hybridization Automation

Abstract

Integrating molecular dynamics for DNA bio- chip fabrication and hybridization automation is promising. The challenge is on obtaining dynamic models for micro- /nano-scale system controls. This paper concerns dynamics of single-stranded DNA molecules tethered to substrate surfaces. A nonlinear control model based on the dynamics model is proposed for DNA bio-chip fabrication and hybridization automation. The contributions of this paper consist of a nonlinear control model for single-stranded DNA molecules tethered to silica surfaces, and integration of the dynamics model for wafer-scale bio-chip fabrication and hybridization automation. I. INTRODUCTION DNA bio-chips discussed in this paper are devices made of less than 100 bases single-stranded DNA molecules tethered to substrate surfaces. Examples of DNA bio-chips include DNA bio-sensors and DNA microarrrays. Dynamics of DNA molecules tethered to surfaces is very important for bio-chip fabrication and hybridization. Unfortunately, most of current understandings of the dynamics take place at micro-level. Many physical observations lack high lateral resolutions in nano-scale for further understanding and miniaturization of the chips. Very little is known about the structure and physical behaviors of DNA molecules and their interactions with substrate surfaces, which are important not only for designing, optimizing DNA bio- chips, but also for controlling dynamics behavior of the DNA molecules during the DNA chip fabrication and hy- bridization processes. During DNA microarray hybridization process, single- stranded DNA molecules find their complimentary se-